The main updates I have for Milestone 2 are: I have ran through the entire vignette and have added analysis throughout, I have increased my sample size to a total of 80 samples, and I have also added Sex as a multiple comparison.
I have imported a total of 80 htseq-count files into a directory, and is displayed in table sampleTable. There are n = 40 from each treatment group in my data file (20 Female, 20 Male for mulitple comparisons).
directory <- "/Users/maricarmen/Desktop/files"
sampleFiles <- grep("treated",list.files(directory),value=TRUE)
sampleCondition <- sub("(.*treated).*","\\1",sampleFiles)
sampleType <- sub(".*treated","",sampleFiles)
sampleTable <- data.frame(sampleName = sampleFiles,
fileName = sampleFiles,
condition = sampleCondition,
type = sampleType)
sampleTable$condition <- factor(sampleTable$condition)
sampleTable$type <- factor(sampleTable$type)
library("DESeq2")
Loading required package: S4Vectors
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Attaching package: ‘BiocGenerics’
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match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min
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see 'citation("Biobase")', and for packages 'citation("pkgname")'.
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ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,
directory = directory,
design= ~ condition)
ddsHTSeq
class: DESeqDataSet
dim: 60483 80
metadata(1): version
assays(1): counts
rownames(60483): ENSG00000000003.13 ENSG00000000005.5 ... ENSGR0000280767.1 ENSGR0000281849.1
rowData names(0):
colnames(80): treatedF_004c60cf-c08e-49df-b4ce-baca41e11250.htseq.counts
treatedF_0d9e4b58-c22f-4de0-8b0d-0b5a8e19a1af.htseq.counts ...
untreatedM_fbbb6d26-8bd4-40da-870b-d8db0f653cfa.htseq.counts
untreatedM_fe76a5ca-f70a-4ab7-b080-5a19ae36dc2b.htseq.counts
colData names(2): condition type
keep <- rowSums(counts(ddsHTSeq)) >= 10
dds <- ddsHTSeq[keep,]
dds$condition <- factor(dds$condition, levels = c("untreated","treated"))
dds <- DESeq(dds)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 4641 genes
-- DESeq argument 'minReplicatesForReplace' = 7
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing
res <- results(dds)
res <- results(dds, name="condition_treated_vs_untreated")
res
log2 fold change (MLE): condition treated vs untreated
Wald test p-value: condition treated vs untreated
DataFrame with 40867 rows and 6 columns
baseMean log2FoldChange lfcSE stat pvalue padj
<numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
ENSG00000000003.13 4453.96587 -0.1997879 0.1850133 -1.0798573 0.280206 0.881472
ENSG00000000005.5 4.40493 -0.1424449 0.5439267 -0.2618826 0.793412 0.985091
ENSG00000000419.11 1164.51323 -0.0883110 0.0897444 -0.9840280 0.325102 0.899680
ENSG00000000457.12 689.51298 0.0034354 0.1243260 0.0276322 0.977955 0.997114
ENSG00000000460.15 341.49032 0.4078734 0.2491110 1.6373160 0.101564 0.727068
... ... ... ... ... ... ...
ENSG00000281904.1 0.217062 -0.188144 0.920972 -0.2042882 0.83812829 NA
ENSG00000281909.1 0.260227 -0.038241 0.809728 -0.0472269 0.96233237 NA
ENSG00000281912.1 58.056910 -0.281619 0.255266 -1.1032368 0.26992436 0.875126
ENSG00000281918.1 0.873386 0.729482 0.619838 1.1768906 0.23923919 NA
ENSG00000281920.1 7.075161 0.899532 0.345914 2.6004500 0.00931016 0.333653
resultsNames(dds)
[1] "Intercept" "condition_treated_vs_untreated"
resLFC <- lfcShrink(dds, coef="condition_treated_vs_untreated", type="apeglm")
using 'apeglm' for LFC shrinkage. If used in published research, please cite:
Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
sequence count data: removing the noise and preserving large differences.
Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895
resLFC
log2 fold change (MAP): condition treated vs untreated
Wald test p-value: condition treated vs untreated
DataFrame with 40867 rows and 5 columns
baseMean log2FoldChange lfcSE pvalue padj
<numeric> <numeric> <numeric> <numeric> <numeric>
ENSG00000000003.13 4453.96587 -4.32659e-06 0.00144265 0.280206 0.881472
ENSG00000000005.5 4.40493 -4.79057e-07 0.00144269 0.793412 0.985091
ENSG00000000419.11 1164.51323 -4.51185e-04 0.00148088 0.325102 0.899680
ENSG00000000457.12 689.51298 1.45701e-05 0.00144263 0.977955 0.997114
ENSG00000000460.15 341.49032 -1.30098e-05 0.00144270 0.101564 0.727068
... ... ... ... ... ...
ENSG00000281904.1 0.217062 -3.84902e-07 0.00144269 0.83812829 NA
ENSG00000281909.1 0.260227 -1.54484e-07 0.00144269 0.96233237 NA
ENSG00000281912.1 58.056910 -4.48092e-06 0.00144268 0.26992436 0.875126
ENSG00000281918.1 0.873386 1.98292e-06 0.00144269 0.23923919 NA
ENSG00000281920.1 7.075161 7.41319e-06 0.00144269 0.00931016 0.333653
resOrdered <- res[order(res$pvalue),]
summary(res)
out of 40851 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up) : 63, 0.15%
LFC < 0 (down) : 138, 0.34%
outliers [1] : 0, 0%
low counts [2] : 15064, 37%
(mean count < 2)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results
sum(res$padj < 0.1, na.rm=TRUE)
[1] 201
res05 <- results(dds, alpha=0.05)
summary(res05)
out of 40851 with nonzero total read count
adjusted p-value < 0.05
LFC > 0 (up) : 27, 0.066%
LFC < 0 (down) : 68, 0.17%
outliers [1] : 0, 0%
low counts [2] : 13480, 33%
(mean count < 1)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results
sum(res05$padj < 0.05, na.rm=TRUE)
[1] 95
plotMA(resLFC, ylim=c(-2,2))
idx <- identify(res$baseMean, res$log2FoldChange)
rownames(res)[idx]
character(0)
resultsNames(dds)
[1] "Intercept" "condition_treated_vs_untreated"
resNorm <- lfcShrink(dds, coef=2, type="normal")
using 'normal' for LFC shrinkage, the Normal prior from Love et al (2014).
Note that type='apeglm' and type='ashr' have shown to have less bias than type='normal'.
See ?lfcShrink for more details on shrinkage type, and the DESeq2 vignette.
Reference: https://doi.org/10.1093/bioinformatics/bty895
resAsh <- lfcShrink(dds, coef=2, type="ashr")
using 'ashr' for LFC shrinkage. If used in published research, please cite:
Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
https://doi.org/10.1093/biostatistics/kxw041
resNorm <- lfcShrink(dds, coef=2, type="normal")
using 'normal' for LFC shrinkage, the Normal prior from Love et al (2014).
Note that type='apeglm' and type='ashr' have shown to have less bias than type='normal'.
See ?lfcShrink for more details on shrinkage type, and the DESeq2 vignette.
Reference: https://doi.org/10.1093/bioinformatics/bty895
resAsh <- lfcShrink(dds, coef=2, type="ashr")
using 'ashr' for LFC shrinkage. If used in published research, please cite:
Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
https://doi.org/10.1093/biostatistics/kxw041
par(mfrow=c(1,3), mar=c(4,4,2,1))
xlim <- c(1,1e5); ylim <- c(-3,3)
plotMA(resLFC, xlim=xlim, ylim=ylim, main="apeglm")
plotMA(resNorm, xlim=xlim, ylim=ylim, main="normal")
plotMA(resAsh, xlim=xlim, ylim=ylim, main="ashr")
plotCounts(dds, gene=which.min(res$padj), intgroup="condition")
d <- plotCounts(dds, gene=which.min(res$padj), intgroup="condition",
returnData=TRUE)
library("ggplot2")
ggplot(d, aes(x=condition, y=count)) +
geom_point(position=position_jitter(w=0.1,h=0)) +
scale_y_log10(breaks=c(25,100,400))
colData(dds)
DataFrame with 80 rows and 4 columns
condition
<factor>
treatedF_004c60cf-c08e-49df-b4ce-baca41e11250.htseq.counts treated
treatedF_0d9e4b58-c22f-4de0-8b0d-0b5a8e19a1af.htseq.counts treated
treatedF_160aee04-df36-4e94-90c5-b01b2991ba48.htseq.counts treated
treatedF_1a228668-b2a0-469f-8801-fdc8be449b44.htseq.counts treated
treatedF_21a0ef5f-24f5-45fe-ac84-deed4ef25329.htseq.counts treated
... ...
untreatedM_d7a9f4a9-6998-45dc-9bc4-06f3f7110429.htseq.counts untreated
untreatedM_e035a46e-6114-4a64-b5ae-9e6209223493.htseq.counts untreated
untreatedM_e208fa4d-3f65-4615-bd6e-870a52bb6da3.htseq.counts untreated
untreatedM_fbbb6d26-8bd4-40da-870b-d8db0f653cfa.htseq.counts untreated
untreatedM_fe76a5ca-f70a-4ab7-b080-5a19ae36dc2b.htseq.counts untreated
type
<factor>
treatedF_004c60cf-c08e-49df-b4ce-baca41e11250.htseq.counts F_004c60cf-c08e-49df-b4ce-baca41e11250.htseq.counts
treatedF_0d9e4b58-c22f-4de0-8b0d-0b5a8e19a1af.htseq.counts F_0d9e4b58-c22f-4de0-8b0d-0b5a8e19a1af.htseq.counts
treatedF_160aee04-df36-4e94-90c5-b01b2991ba48.htseq.counts F_160aee04-df36-4e94-90c5-b01b2991ba48.htseq.counts
treatedF_1a228668-b2a0-469f-8801-fdc8be449b44.htseq.counts F_1a228668-b2a0-469f-8801-fdc8be449b44.htseq.counts
treatedF_21a0ef5f-24f5-45fe-ac84-deed4ef25329.htseq.counts F_21a0ef5f-24f5-45fe-ac84-deed4ef25329.htseq.counts
... ...
untreatedM_d7a9f4a9-6998-45dc-9bc4-06f3f7110429.htseq.counts M_d7a9f4a9-6998-45dc-9bc4-06f3f7110429.htseq.counts
untreatedM_e035a46e-6114-4a64-b5ae-9e6209223493.htseq.counts M_e035a46e-6114-4a64-b5ae-9e6209223493.htseq.counts
untreatedM_e208fa4d-3f65-4615-bd6e-870a52bb6da3.htseq.counts M_e208fa4d-3f65-4615-bd6e-870a52bb6da3.htseq.counts
untreatedM_fbbb6d26-8bd4-40da-870b-d8db0f653cfa.htseq.counts M_fbbb6d26-8bd4-40da-870b-d8db0f653cfa.htseq.counts
untreatedM_fe76a5ca-f70a-4ab7-b080-5a19ae36dc2b.htseq.counts M_fe76a5ca-f70a-4ab7-b080-5a19ae36dc2b.htseq.counts
sizeFactor replaceable
<numeric> <logical>
treatedF_004c60cf-c08e-49df-b4ce-baca41e11250.htseq.counts 0.524686 TRUE
treatedF_0d9e4b58-c22f-4de0-8b0d-0b5a8e19a1af.htseq.counts 0.945973 TRUE
treatedF_160aee04-df36-4e94-90c5-b01b2991ba48.htseq.counts 0.766143 TRUE
treatedF_1a228668-b2a0-469f-8801-fdc8be449b44.htseq.counts 1.999997 TRUE
treatedF_21a0ef5f-24f5-45fe-ac84-deed4ef25329.htseq.counts 1.271887 TRUE
... ... ...
untreatedM_d7a9f4a9-6998-45dc-9bc4-06f3f7110429.htseq.counts 0.995618 TRUE
untreatedM_e035a46e-6114-4a64-b5ae-9e6209223493.htseq.counts 1.157396 TRUE
untreatedM_e208fa4d-3f65-4615-bd6e-870a52bb6da3.htseq.counts 1.358135 TRUE
untreatedM_fbbb6d26-8bd4-40da-870b-d8db0f653cfa.htseq.counts 0.406704 TRUE
untreatedM_fe76a5ca-f70a-4ab7-b080-5a19ae36dc2b.htseq.counts 0.653657 TRUE
ddsMF <- dds
levels(ddsMF$type)
[1] "F_004c60cf-c08e-49df-b4ce-baca41e11250.htseq.counts"
[2] "F_0d9e4b58-c22f-4de0-8b0d-0b5a8e19a1af.htseq.counts"
[3] "F_104c7c7e-583a-4496-a685-5d277e28c11b.htseq.counts"
[4] "F_10a32136-8a4d-4af3-8e70-543b2a336c91.htseq.counts"
[5] "F_160aee04-df36-4e94-90c5-b01b2991ba48.htseq.counts"
[6] "F_16fc8611-259d-4cd8-9e93-60d97bebb6bf.htseq.counts"
[7] "F_1a228668-b2a0-469f-8801-fdc8be449b44.htseq.counts"
[8] "F_21a0ef5f-24f5-45fe-ac84-deed4ef25329.htseq.counts"
[9] "F_28ef84e7-f566-40a7-b239-26d3e23c878a.htseq.counts"
[10] "F_2baabd07-b92c-4ac1-8de7-3d8df4f4a80b.htseq.counts"
[11] "F_2f3f2e57-4c69-469f-be9c-01cc4f704427.htseq.counts"
[12] "F_3e0831c0-6726-4f71-9cba-faaeea280cf9.htseq.counts"
[13] "F_554f6de3-63c7-47b1-a75a-dcfc73f54e96.htseq.counts"
[14] "F_6c86f9ae-9e88-4eae-9ba3-4866943cca7f.htseq.counts"
[15] "F_6cd9b90b-0c6c-44bd-8536-5a93553a7730.htseq.counts"
[16] "F_73756e81-79a2-4bff-96e7-99f038306b3e.htseq.counts"
[17] "F_7a3a131b-883d-4f82-8b3b-ede7733f68d8.htseq.counts"
[18] "F_7b77e8cb-3f1d-4af7-b609-d75f912484c4.htseq.counts"
[19] "F_89e20bd9-15e5-48e6-9dfe-0b919c817216.htseq.counts"
[20] "F_8d78e34d-490b-4f2e-ba1a-427afe96d26e.htseq.counts"
[21] "F_92ee9ee1-8f03-4b53-b6c2-04d22fd692ae.htseq.counts"
[22] "F_98380eb7-4de1-4e3a-989c-eedf6eec2977.htseq.counts"
[23] "F_99e82612-a602-459b-8a60-80a812bf9d88.htseq.counts"
[24] "F_9ccd91ba-7180-443a-b03b-f9b398c679e4.htseq.counts"
[25] "F_aaec3912-230f-4418-986d-878e77480f94.htseq.counts"
[26] "F_b39bcb10-164d-48c5-89ba-9ef668765db6.htseq.counts"
[27] "F_b49faa57-5a15-4193-9552-130d9a63eb40.htseq.counts"
[28] "F_d2bf6185-08a5-4a73-9f87-7164cca1ccf6.htseq.counts"
[29] "F_d5fd715a-cf6d-4b29-ad9d-b3e58c55262a.htseq.counts"
[30] "F_edf02d6d-619f-4325-a585-dca7bf5afbeb.htseq.counts"
[31] "F_ee857c4c-e6a9-4f39-b95b-20fe46dd1ab7.htseq.counts"
[32] "F_eea3fcee-ee51-461b-abb4-c393c084e018.htseq.counts"
[33] "F_eed21a5a-30db-45a0-9b60-3f6a91b38cb6.htseq.counts"
[34] "F_f6ae6ac1-3e00-4021-a6e7-fbb0d5f12836.htseq.counts"
[35] "F_f7a956f8-4dc2-437a-92db-8baf8f9b3f14.htseq.counts"
[36] "F_ffeed225-c2a3-4b4c-954c-4816903782a9.htseq.counts"
[37] "M_04e7f1a4-3173-4a6f-af60-04e1f2e29868.htseq.counts"
[38] "M_05ac7b05-e459-4833-97fc-530185a7a55f.htseq.counts"
[39] "M_063411ca-874c-49ff-85c2-b6946f43df4e.htseq.counts"
[40] "M_09f395dd-d007-41e0-8a51-a6533ae51087.htseq.counts"
[41] "M_10d6deec-fd89-4115-92f5-c9def40428b5.htseq.counts"
[42] "M_1c6bb58a-3869-41f5-9fef-9070bbfedbad.htseq.counts"
[43] "M_1d782a72-61f3-4002-bee5-67daeb8244e3.htseq.counts"
[44] "M_2cc2e3ce-68cd-4690-9fff-5ecf86c2f57a.htseq.counts"
[45] "M_35a2858e-9787-457c-9435-33bd62332aa3.htseq.counts"
[46] "M_51c2d807-7ee6-4b42-a6a7-3eb14f987bc0.htseq.counts"
[47] "M_57ef7745-338c-4fb2-ac9b-9f57daba2c51.htseq.counts"
[48] "M_77b9a94e-aaa7-409c-9849-86ba7d5c061a.htseq.counts"
[49] "M_78e27399-eb4a-4b86-992e-3e052bad044c.htseq.counts"
[50] "M_79f4b12a-ed1c-46d5-ae3d-a0422454eaf4.htseq.counts"
[51] "M_7f86ace4-9a17-4b17-8a79-3b2ef53f62c3.htseq.counts"
[52] "M_89eb1fc8-6b38-446e-a4b0-fb9c520298dc.htseq.counts"
[53] "M_9700948e-21f5-42ae-9cb5-f18c745887ce.htseq.counts"
[54] "M_a3a6543b-ea79-4724-a140-c83392b1842b.htseq.counts"
[55] "M_ad69efb1-61ab-4492-8468-9006dd00e915.htseq.counts"
[56] "M_b04fb368-4b93-4ef9-ae9f-020484c1686b.htseq.counts"
[57] "M_b1820867-e6b2-4228-ad00-19d1d7fddf67.htseq.counts"
[58] "M_b5d92dd1-d98b-4b9e-953e-81c04dfb1e0d.htseq.counts"
[59] "M_bdd35388-0850-40ac-a21a-6bfee0c34eef.htseq.counts"
[60] "M_c49c187f-98e7-463d-a18b-accf3205eb81.htseq.counts"
[61] "M_c4c4578a-f1c2-462a-873f-c8db84fe3a6f.htseq.counts"
[62] "M_c7e1465f-cc5a-4dc9-9bb1-6f1112da7aad.htseq.counts"
[63] "M_cfb40dba-37a7-4ae7-a2c9-34becc30f939.htseq.counts"
[64] "M_d1cbb686-93d8-4349-8bf5-756887c60ebc.htseq.counts"
[65] "M_d7a9f4a9-6998-45dc-9bc4-06f3f7110429.htseq.counts"
[66] "M_dad3353e-6721-4e2e-ae06-04eea4c00f12.htseq.counts"
[67] "M_dcf5a350-7cff-475a-8f53-376422f990eb.htseq.counts"
[68] "M_e035a46e-6114-4a64-b5ae-9e6209223493.htseq.counts"
[69] "M_e208fa4d-3f65-4615-bd6e-870a52bb6da3.htseq.counts"
[70] "M_e48c520a-d62c-440d-b17c-5b5ff03d41a2.htseq.counts"
[71] "M_e4d48564-e021-4bbc-bc00-145e9d64b501.htseq.counts"
[72] "M_fbbb6d26-8bd4-40da-870b-d8db0f653cfa.htseq.counts"
[73] "M_fe76a5ca-f70a-4ab7-b080-5a19ae36dc2b.htseq.counts"
levels(ddsMF$type) <- sub("_.*", "", levels(ddsMF$type))
levels(ddsMF$type)
[1] "F" "M"
design(ddsMF) <- formula(~ type + condition)
ddsMF <- DESeq(ddsMF)
using pre-existing size factors
estimating dispersions
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 4721 genes
-- DESeq argument 'minReplicatesForReplace' = 7
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing
resMF <- results(ddsMF)
head(resMF)
log2 fold change (MLE): condition treated vs untreated
Wald test p-value: condition treated vs untreated
DataFrame with 6 rows and 6 columns
baseMean log2FoldChange lfcSE stat pvalue padj
<numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
ENSG00000000003.13 4453.96587 -0.2138352 0.1814214 -1.178666 0.238531 0.838756
ENSG00000000005.5 4.40493 -0.1681652 0.5402803 -0.311256 0.755606 0.974777
ENSG00000000419.11 1164.51323 -0.0888392 0.0901364 -0.985609 0.324325 0.878919
ENSG00000000457.12 689.51298 0.0206650 0.1233242 0.167567 0.866924 0.988850
ENSG00000000460.15 341.49032 0.3933651 0.2501419 1.572568 0.115819 0.716756
ENSG00000000938.11 272.32558 0.0680974 0.2307494 0.295114 0.767907 0.976718
resMFType <- results(ddsMF,
contrast=c("type", "F", "M"))
head(resMFType)
log2 fold change (MLE): type F vs M
Wald test p-value: type F vs M
DataFrame with 6 rows and 6 columns
baseMean log2FoldChange lfcSE stat pvalue padj
<numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
ENSG00000000003.13 4453.96587 -0.3789700 0.1814214 -2.088894 0.0367173 0.1511632
ENSG00000000005.5 4.40493 0.8600421 0.5405167 1.591148 0.1115763 0.2963857
ENSG00000000419.11 1164.51323 0.0383597 0.0901364 0.425573 0.6704187 0.8258209
ENSG00000000457.12 689.51298 0.1835394 0.1233242 1.488267 0.1366805 0.3335258
ENSG00000000460.15 341.49032 -0.0914826 0.2501418 -0.365723 0.7145719 0.8516444
ENSG00000000938.11 272.32558 0.5433143 0.2307498 2.354561 0.0185446 0.0985477
mcols(res)$description
[1] "mean of normalized counts for all samples"
[2] "log2 fold change (MLE): condition treated vs untreated"
[3] "standard error: condition treated vs untreated"
[4] "Wald statistic: condition treated vs untreated"
[5] "Wald test p-value: condition treated vs untreated"
[6] "BH adjusted p-values"
write.csv(as.data.frame(resOrdered),
file="condition_treated_results.csv")
vsd <- vst(dds, blind=FALSE)
rld <- rlog(dds, blind=FALSE)
rlog() may take a long time with 50 or more samples,
vst() is a much faster transformation
head(assay(vsd), 3)
treatedF_004c60cf-c08e-49df-b4ce-baca41e11250.htseq.counts
ENSG00000000003.13 12.010108
ENSG00000000005.5 3.803133
ENSG00000000419.11 9.624601
treatedF_0d9e4b58-c22f-4de0-8b0d-0b5a8e19a1af.htseq.counts
ENSG00000000003.13 12.000345
ENSG00000000005.5 3.837895
ENSG00000000419.11 10.065377
treatedF_160aee04-df36-4e94-90c5-b01b2991ba48.htseq.counts
ENSG00000000003.13 12.133125
ENSG00000000005.5 4.344518
ENSG00000000419.11 10.088965
treatedF_1a228668-b2a0-469f-8801-fdc8be449b44.htseq.counts
ENSG00000000003.13 12.126734
ENSG00000000005.5 3.480745
ENSG00000000419.11 10.358151
treatedF_21a0ef5f-24f5-45fe-ac84-deed4ef25329.htseq.counts
ENSG00000000003.13 11.335300
ENSG00000000005.5 3.137687
ENSG00000000419.11 10.327496
treatedF_28ef84e7-f566-40a7-b239-26d3e23c878a.htseq.counts
ENSG00000000003.13 9.669128
ENSG00000000005.5 3.677303
ENSG00000000419.11 9.877421
treatedF_2baabd07-b92c-4ac1-8de7-3d8df4f4a80b.htseq.counts
ENSG00000000003.13 11.031863
ENSG00000000005.5 3.776332
ENSG00000000419.11 10.265872
treatedF_3e0831c0-6726-4f71-9cba-faaeea280cf9.htseq.counts
ENSG00000000003.13 11.382912
ENSG00000000005.5 3.724349
ENSG00000000419.11 10.583432
treatedF_554f6de3-63c7-47b1-a75a-dcfc73f54e96.htseq.counts
ENSG00000000003.13 11.690293
ENSG00000000005.5 3.137687
ENSG00000000419.11 11.313958
treatedF_6cd9b90b-0c6c-44bd-8536-5a93553a7730.htseq.counts
ENSG00000000003.13 12.533113
ENSG00000000005.5 4.553765
ENSG00000000419.11 10.464822
treatedF_7a3a131b-883d-4f82-8b3b-ede7733f68d8.htseq.counts
ENSG00000000003.13 12.011736
ENSG00000000005.5 3.786213
ENSG00000000419.11 10.395398
treatedF_7b77e8cb-3f1d-4af7-b609-d75f912484c4.htseq.counts
ENSG00000000003.13 10.259599
ENSG00000000005.5 3.137687
ENSG00000000419.11 9.829390
treatedF_89e20bd9-15e5-48e6-9dfe-0b919c817216.htseq.counts
ENSG00000000003.13 10.670326
ENSG00000000005.5 3.137687
ENSG00000000419.11 9.485302
treatedF_98380eb7-4de1-4e3a-989c-eedf6eec2977.htseq.counts
ENSG00000000003.13 12.086947
ENSG00000000005.5 6.089224
ENSG00000000419.11 10.167475
treatedF_9ccd91ba-7180-443a-b03b-f9b398c679e4.htseq.counts
ENSG00000000003.13 12.120421
ENSG00000000005.5 4.456754
ENSG00000000419.11 10.003843
treatedF_aaec3912-230f-4418-986d-878e77480f94.htseq.counts
ENSG00000000003.13 12.558911
ENSG00000000005.5 4.416152
ENSG00000000419.11 10.712649
treatedF_d5fd715a-cf6d-4b29-ad9d-b3e58c55262a.htseq.counts
ENSG00000000003.13 11.694173
ENSG00000000005.5 3.137687
ENSG00000000419.11 9.941086
treatedF_ee857c4c-e6a9-4f39-b95b-20fe46dd1ab7.htseq.counts
ENSG00000000003.13 12.068945
ENSG00000000005.5 4.714298
ENSG00000000419.11 10.060595
treatedF_eea3fcee-ee51-461b-abb4-c393c084e018.htseq.counts
ENSG00000000003.13 11.723174
ENSG00000000005.5 4.270978
ENSG00000000419.11 9.465239
treatedF_f6ae6ac1-3e00-4021-a6e7-fbb0d5f12836.htseq.counts
ENSG00000000003.13 10.984981
ENSG00000000005.5 3.541637
ENSG00000000419.11 9.541770
treatedM_04e7f1a4-3173-4a6f-af60-04e1f2e29868.htseq.counts
ENSG00000000003.13 11.423792
ENSG00000000005.5 3.572102
ENSG00000000419.11 10.055809
treatedM_05ac7b05-e459-4833-97fc-530185a7a55f.htseq.counts
ENSG00000000003.13 13.510874
ENSG00000000005.5 3.776884
ENSG00000000419.11 9.737111
treatedM_063411ca-874c-49ff-85c2-b6946f43df4e.htseq.counts
ENSG00000000003.13 13.225876
ENSG00000000005.5 3.860305
ENSG00000000419.11 10.978271
treatedM_1c6bb58a-3869-41f5-9fef-9070bbfedbad.htseq.counts
ENSG00000000003.13 10.819752
ENSG00000000005.5 4.079125
ENSG00000000419.11 10.276796
treatedM_51c2d807-7ee6-4b42-a6a7-3eb14f987bc0.htseq.counts
ENSG00000000003.13 11.625170
ENSG00000000005.5 3.137687
ENSG00000000419.11 9.747406
treatedM_57ef7745-338c-4fb2-ac9b-9f57daba2c51.htseq.counts
ENSG00000000003.13 12.875045
ENSG00000000005.5 4.597585
ENSG00000000419.11 10.166994
treatedM_77b9a94e-aaa7-409c-9849-86ba7d5c061a.htseq.counts
ENSG00000000003.13 11.338110
ENSG00000000005.5 3.137687
ENSG00000000419.11 9.763866
treatedM_79f4b12a-ed1c-46d5-ae3d-a0422454eaf4.htseq.counts
ENSG00000000003.13 11.247954
ENSG00000000005.5 3.583671
ENSG00000000419.11 9.949941
treatedM_7f86ace4-9a17-4b17-8a79-3b2ef53f62c3.htseq.counts
ENSG00000000003.13 11.281103
ENSG00000000005.5 3.823859
ENSG00000000419.11 9.770897
treatedM_9700948e-21f5-42ae-9cb5-f18c745887ce.htseq.counts
ENSG00000000003.13 12.448792
ENSG00000000005.5 3.137687
ENSG00000000419.11 9.848389
treatedM_a3a6543b-ea79-4724-a140-c83392b1842b.htseq.counts
ENSG00000000003.13 12.15704
ENSG00000000005.5 3.70595
ENSG00000000419.11 10.27649
treatedM_b5d92dd1-d98b-4b9e-953e-81c04dfb1e0d.htseq.counts
ENSG00000000003.13 11.642861
ENSG00000000005.5 3.137687
ENSG00000000419.11 10.132197
treatedM_bdd35388-0850-40ac-a21a-6bfee0c34eef.htseq.counts
ENSG00000000003.13 11.690043
ENSG00000000005.5 4.143037
ENSG00000000419.11 10.299080
treatedM_c49c187f-98e7-463d-a18b-accf3205eb81.htseq.counts
ENSG00000000003.13 12.425289
ENSG00000000005.5 4.843572
ENSG00000000419.11 10.249863
treatedM_c4c4578a-f1c2-462a-873f-c8db84fe3a6f.htseq.counts
ENSG00000000003.13 11.523250
ENSG00000000005.5 3.897876
ENSG00000000419.11 9.993003
treatedM_c7e1465f-cc5a-4dc9-9bb1-6f1112da7aad.htseq.counts
ENSG00000000003.13 11.443496
ENSG00000000005.5 4.585825
ENSG00000000419.11 10.471124
treatedM_dad3353e-6721-4e2e-ae06-04eea4c00f12.htseq.counts
ENSG00000000003.13 11.551448
ENSG00000000005.5 3.714484
ENSG00000000419.11 10.152403
treatedM_dcf5a350-7cff-475a-8f53-376422f990eb.htseq.counts
ENSG00000000003.13 12.082464
ENSG00000000005.5 3.137687
ENSG00000000419.11 9.578542
treatedM_e48c520a-d62c-440d-b17c-5b5ff03d41a2.htseq.counts
ENSG00000000003.13 13.902529
ENSG00000000005.5 3.610941
ENSG00000000419.11 10.094763
treatedM_e4d48564-e021-4bbc-bc00-145e9d64b501.htseq.counts
ENSG00000000003.13 11.341795
ENSG00000000005.5 3.564775
ENSG00000000419.11 10.217635
untreatedF_0d9e4b58-c22f-4de0-8b0d-0b5a8e19a1af.htseq.counts
ENSG00000000003.13 12.000345
ENSG00000000005.5 3.837895
ENSG00000000419.11 10.065377
untreatedF_104c7c7e-583a-4496-a685-5d277e28c11b.htseq.counts
ENSG00000000003.13 12.182466
ENSG00000000005.5 3.137687
ENSG00000000419.11 11.221385
untreatedF_10a32136-8a4d-4af3-8e70-543b2a336c91.htseq.counts
ENSG00000000003.13 11.952164
ENSG00000000005.5 3.137687
ENSG00000000419.11 10.266446
untreatedF_16fc8611-259d-4cd8-9e93-60d97bebb6bf.htseq.counts
ENSG00000000003.13 12.141786
ENSG00000000005.5 3.137687
ENSG00000000419.11 10.424273
untreatedF_21a0ef5f-24f5-45fe-ac84-deed4ef25329.htseq.counts
ENSG00000000003.13 11.335300
ENSG00000000005.5 3.137687
ENSG00000000419.11 10.327496
untreatedF_2f3f2e57-4c69-469f-be9c-01cc4f704427.htseq.counts
ENSG00000000003.13 12.671569
ENSG00000000005.5 4.177815
ENSG00000000419.11 10.310761
untreatedF_3e0831c0-6726-4f71-9cba-faaeea280cf9.htseq.counts
ENSG00000000003.13 11.382912
ENSG00000000005.5 3.724349
ENSG00000000419.11 10.583432
untreatedF_6c86f9ae-9e88-4eae-9ba3-4866943cca7f.htseq.counts
ENSG00000000003.13 12.413538
ENSG00000000005.5 3.137687
ENSG00000000419.11 10.151889
untreatedF_73756e81-79a2-4bff-96e7-99f038306b3e.htseq.counts
ENSG00000000003.13 12.522536
ENSG00000000005.5 3.874868
ENSG00000000419.11 10.174565
untreatedF_8d78e34d-490b-4f2e-ba1a-427afe96d26e.htseq.counts
ENSG00000000003.13 11.897977
ENSG00000000005.5 3.595631
ENSG00000000419.11 9.494392
untreatedF_92ee9ee1-8f03-4b53-b6c2-04d22fd692ae.htseq.counts
ENSG00000000003.13 9.749285
ENSG00000000005.5 5.058470
ENSG00000000419.11 10.549118
untreatedF_98380eb7-4de1-4e3a-989c-eedf6eec2977.htseq.counts
ENSG00000000003.13 12.086947
ENSG00000000005.5 6.089224
ENSG00000000419.11 10.167475
untreatedF_99e82612-a602-459b-8a60-80a812bf9d88.htseq.counts
ENSG00000000003.13 11.342236
ENSG00000000005.5 5.220944
ENSG00000000419.11 10.238865
untreatedF_b39bcb10-164d-48c5-89ba-9ef668765db6.htseq.counts
ENSG00000000003.13 12.901341
ENSG00000000005.5 4.440781
ENSG00000000419.11 10.177789
untreatedF_b49faa57-5a15-4193-9552-130d9a63eb40.htseq.counts
ENSG00000000003.13 11.730460
ENSG00000000005.5 3.137687
ENSG00000000419.11 9.949948
untreatedF_d2bf6185-08a5-4a73-9f87-7164cca1ccf6.htseq.counts
ENSG00000000003.13 13.229894
ENSG00000000005.5 3.952792
ENSG00000000419.11 9.967647
untreatedF_edf02d6d-619f-4325-a585-dca7bf5afbeb.htseq.counts
ENSG00000000003.13 12.058079
ENSG00000000005.5 3.137687
ENSG00000000419.11 10.150240
untreatedF_eed21a5a-30db-45a0-9b60-3f6a91b38cb6.htseq.counts
ENSG00000000003.13 7.528241
ENSG00000000005.5 3.137687
ENSG00000000419.11 10.025289
untreatedF_f7a956f8-4dc2-437a-92db-8baf8f9b3f14.htseq.counts
ENSG00000000003.13 12.612583
ENSG00000000005.5 3.137687
ENSG00000000419.11 9.672198
untreatedF_ffeed225-c2a3-4b4c-954c-4816903782a9.htseq.counts
ENSG00000000003.13 11.700559
ENSG00000000005.5 3.697129
ENSG00000000419.11 10.189830
untreatedM_09f395dd-d007-41e0-8a51-a6533ae51087.htseq.counts
ENSG00000000003.13 13.140656
ENSG00000000005.5 3.137687
ENSG00000000419.11 10.268505
untreatedM_10d6deec-fd89-4115-92f5-c9def40428b5.htseq.counts
ENSG00000000003.13 12.800665
ENSG00000000005.5 3.137687
ENSG00000000419.11 10.260551
untreatedM_1d782a72-61f3-4002-bee5-67daeb8244e3.htseq.counts
ENSG00000000003.13 13.627063
ENSG00000000005.5 5.388573
ENSG00000000419.11 10.837103
untreatedM_2cc2e3ce-68cd-4690-9fff-5ecf86c2f57a.htseq.counts
ENSG00000000003.13 11.88208
ENSG00000000005.5 4.82894
ENSG00000000419.11 10.26352
untreatedM_35a2858e-9787-457c-9435-33bd62332aa3.htseq.counts
ENSG00000000003.13 10.86300
ENSG00000000005.5 4.02441
ENSG00000000419.11 10.10995
untreatedM_78e27399-eb4a-4b86-992e-3e052bad044c.htseq.counts
ENSG00000000003.13 11.439581
ENSG00000000005.5 3.765704
ENSG00000000419.11 9.705612
untreatedM_89eb1fc8-6b38-446e-a4b0-fb9c520298dc.htseq.counts
ENSG00000000003.13 12.639202
ENSG00000000005.5 3.622842
ENSG00000000419.11 10.615463
untreatedM_9700948e-21f5-42ae-9cb5-f18c745887ce.htseq.counts
ENSG00000000003.13 12.448792
ENSG00000000005.5 3.137687
ENSG00000000419.11 9.848389
untreatedM_a3a6543b-ea79-4724-a140-c83392b1842b.htseq.counts
ENSG00000000003.13 12.15704
ENSG00000000005.5 3.70595
ENSG00000000419.11 10.27649
untreatedM_ad69efb1-61ab-4492-8468-9006dd00e915.htseq.counts
ENSG00000000003.13 11.240405
ENSG00000000005.5 3.137687
ENSG00000000419.11 10.093893
untreatedM_b04fb368-4b93-4ef9-ae9f-020484c1686b.htseq.counts
ENSG00000000003.13 11.950998
ENSG00000000005.5 3.137687
ENSG00000000419.11 9.683769
untreatedM_b1820867-e6b2-4228-ad00-19d1d7fddf67.htseq.counts
ENSG00000000003.13 12.825720
ENSG00000000005.5 4.104038
ENSG00000000419.11 10.936106
untreatedM_bdd35388-0850-40ac-a21a-6bfee0c34eef.htseq.counts
ENSG00000000003.13 11.690043
ENSG00000000005.5 4.143037
ENSG00000000419.11 10.299080
untreatedM_cfb40dba-37a7-4ae7-a2c9-34becc30f939.htseq.counts
ENSG00000000003.13 11.807158
ENSG00000000005.5 3.137687
ENSG00000000419.11 9.561400
untreatedM_d1cbb686-93d8-4349-8bf5-756887c60ebc.htseq.counts
ENSG00000000003.13 12.862365
ENSG00000000005.5 3.137687
ENSG00000000419.11 10.587888
untreatedM_d7a9f4a9-6998-45dc-9bc4-06f3f7110429.htseq.counts
ENSG00000000003.13 12.157830
ENSG00000000005.5 3.820541
ENSG00000000419.11 9.799839
untreatedM_e035a46e-6114-4a64-b5ae-9e6209223493.htseq.counts
ENSG00000000003.13 11.865715
ENSG00000000005.5 3.771832
ENSG00000000419.11 10.103464
untreatedM_e208fa4d-3f65-4615-bd6e-870a52bb6da3.htseq.counts
ENSG00000000003.13 12.020334
ENSG00000000005.5 3.553532
ENSG00000000419.11 10.590308
untreatedM_fbbb6d26-8bd4-40da-870b-d8db0f653cfa.htseq.counts
ENSG00000000003.13 12.779825
ENSG00000000005.5 4.192442
ENSG00000000419.11 10.385769
untreatedM_fe76a5ca-f70a-4ab7-b080-5a19ae36dc2b.htseq.counts
ENSG00000000003.13 11.681830
ENSG00000000005.5 4.158100
ENSG00000000419.11 9.794419
# this gives log2(n + 1)
ntd <- normTransform(dds)
library("vsn")
meanSdPlot(assay(ntd))
meanSdPlot(assay(vsd))
meanSdPlot(assay(rld))
library("pheatmap")
select <- order(rowMeans(counts(ddsMF,normalized=TRUE)),
decreasing=TRUE)[1:20]
df <- as.data.frame(colData(ddsMF)[,c("condition","type")])
pheatmap(assay(ntd)[select,], cluster_rows=FALSE, show_rownames=FALSE, show_colnames = FALSE,
cluster_cols=FALSE, annotation_col=df)
library("pheatmap")
select <- order(rowMeans(counts(dds,normalized=TRUE)),
decreasing=TRUE)[1:20]
df <- as.data.frame(colData(ddsMF)[,c("condition","type")])
pheatmap(assay(ntd)[select,], cluster_rows=FALSE, show_rownames=FALSE, show_colnames = FALSE,
cluster_cols=FALSE, annotation_col=df)
pheatmap(assay(vsd)[select,], cluster_rows=FALSE, show_rownames=FALSE, show_colnames = FALSE,
cluster_cols=FALSE, annotation_col=df)
pheatmap(assay(rld)[select,], cluster_rows=FALSE, show_rownames=FALSE, show_colnames = FALSE,
cluster_cols=FALSE, annotation_col=df)
sampleDists <- dist(t(assay(vsd)))
library("pheatmap")
library("RColorBrewer")
sampleDistMatrix <- as.matrix(sampleDists)
rownames(sampleDistMatrix) <- paste(vsd$condition)
colnames(sampleDistMatrix) <- NULL
colors <- colorRampPalette( rev(brewer.pal(9, "Blues")) )(255)
pheatmap(sampleDistMatrix,
clustering_distance_rows=sampleDists,
clustering_distance_cols=sampleDists,
col=colors)
plotPCA(vsd, intgroup="condition", ntop = 500, returnData = FALSE)
dds <- estimateSizeFactors(dds)
dds <- estimateDispersions(dds)
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
dds <- nbinomWaldTest(dds)
resultsNames(dds)
[1] "Intercept" "condition_treated_vs_untreated"
dds <- DESeq(dds, test="LRT", reduced=~1)
using pre-existing size factors
estimating dispersions
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 4685 genes
-- DESeq argument 'minReplicatesForReplace' = 7
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing
res <- results(dds)
resApeT <- lfcShrink(dds, coef=2, type="apeglm", lfcThreshold=1)
using 'apeglm' for LFC shrinkage. If used in published research, please cite:
Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
sequence count data: removing the noise and preserving large differences.
Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895
computing FSOS 'false sign or small' s-values (T=1)
plotMA(resApeT, ylim=c(-3,3), cex=.8)
thresholding s-values on alpha=0.005 to color points
abline(h=c(-1,1), col="dodgerblue", lwd=2)
summary(res)
out of 40852 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up) : 42, 0.1%
LFC < 0 (down) : 105, 0.26%
outliers [1] : 0, 0%
low counts [2] : 15855, 39%
(mean count < 2)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results
plotDispEsts(dds)
ddsCustom <- dds
useForMedian <- mcols(ddsCustom)$dispGeneEst > 1e-7
medianDisp <- median(mcols(ddsCustom)$dispGeneEst[useForMedian],
na.rm=TRUE)
dispersionFunction(ddsCustom) <- function(mu) medianDisp
ddsCustom <- estimateDispersionsMAP(ddsCustom)
found already estimated dispersions, removing these
metadata(res)$alpha
[1] 0.1
metadata(res)$filterThreshold
38.79723%
2.252725
ddsCustom <- dds
useForMedian <- mcols(ddsCustom)$dispGeneEst > 1e-7
medianDisp <- median(mcols(ddsCustom)$dispGeneEst[useForMedian],
na.rm=TRUE)
dispersionFunction(ddsCustom) <- function(mu) medianDisp
ddsCustom <- estimateDispersionsMAP(ddsCustom)
found already estimated dispersions, removing these
plot(metadata(res)$filterNumRej,
type="b", ylab="number of rejections",
xlab="quantiles of filter")
lines(metadata(res)$lo.fit, col="red")
abline(v=metadata(res)$filterTheta)
resNoFilt <- results(dds, independentFiltering=FALSE)
addmargins(table(filtering=(res$padj < .1),
noFiltering=(resNoFilt$padj < .1)))
noFiltering
filtering FALSE TRUE Sum
FALSE 24865 0 24865
TRUE 66 81 147
Sum 24931 81 25012
par(mfrow=c(2,2),mar=c(2,2,1,1))
ylim <- c(-2.5,2.5)
resGA <- results(dds, lfcThreshold=.5, altHypothesis="greaterAbs")
resLA <- results(dds, lfcThreshold=.5, altHypothesis="lessAbs")
resG <- results(dds, lfcThreshold=.5, altHypothesis="greater")
resL <- results(dds, lfcThreshold=.5, altHypothesis="less")
drawLines <- function() abline(h=c(-.5,.5),col="dodgerblue",lwd=2)
plotMA(resGA, ylim=ylim); drawLines()
plotMA(resLA, ylim=ylim); drawLines()
plotMA(resG, ylim=ylim); drawLines()
plotMA(resL, ylim=ylim); drawLines()
mcols(dds,use.names=TRUE)[1:4,1:4]
DataFrame with 4 rows and 4 columns
baseMean baseVar allZero dispGeneEst
<numeric> <numeric> <logical> <numeric>
ENSG00000000003.13 4453.96587 6.80235e+06 FALSE 0.3426609
ENSG00000000005.5 4.40493 8.25872e+01 FALSE 2.6284098
ENSG00000000419.11 1164.51323 1.16676e+05 FALSE 0.0724843
ENSG00000000457.12 689.51298 7.08616e+04 FALSE 0.1475156
substr(names(mcols(dds)),1,10)
[1] "baseMean" "baseVar" "allZero" "dispGeneEs" "dispGeneIt" "dispFit" "dispersion" "dispIter"
[9] "dispOutlie" "dispMAP" "Intercept" "condition_" "SE_Interce" "SE_conditi" "WaldStatis" "WaldStatis"
[17] "WaldPvalue" "WaldPvalue" "betaConv" "betaIter" "deviance" "maxCooks"
mcols(mcols(dds), use.names=TRUE)[1:4,]
DataFrame with 4 rows and 2 columns
type description
<character> <character>
baseMean intermediate mean of normalized c..
baseVar intermediate variance of normaliz..
allZero intermediate all counts for a gen..
dispGeneEst intermediate gene-wise estimates ..
head(assays(dds)[["mu"]])
treatedF_004c60cf-c08e-49df-b4ce-baca41e11250.htseq.counts
ENSG00000000003.13 2175.258337
ENSG00000000005.5 2.179508
ENSG00000000419.11 592.427923
ENSG00000000457.12 362.263636
ENSG00000000460.15 204.425909
ENSG00000000938.11 148.032876
treatedF_0d9e4b58-c22f-4de0-8b0d-0b5a8e19a1af.htseq.counts
ENSG00000000003.13 3921.840178
ENSG00000000005.5 3.929502
ENSG00000000419.11 1068.106529
ENSG00000000457.12 653.136255
ENSG00000000460.15 368.565761
ENSG00000000938.11 266.893026
treatedF_160aee04-df36-4e94-90c5-b01b2991ba48.htseq.counts
ENSG00000000003.13 3176.2943
ENSG00000000005.5 3.1825
ENSG00000000419.11 865.0584
ENSG00000000457.12 528.9744
ENSG00000000460.15 298.5010
ENSG00000000938.11 216.1564
treatedF_1a228668-b2a0-469f-8801-fdc8be449b44.htseq.counts
ENSG00000000003.13 8291.641686
ENSG00000000005.5 8.307841
ENSG00000000419.11 2258.214567
ENSG00000000457.12 1380.875189
ENSG00000000460.15 779.229924
ENSG00000000938.11 564.271169
treatedF_21a0ef5f-24f5-45fe-ac84-deed4ef25329.htseq.counts
ENSG00000000003.13 5273.023466
ENSG00000000005.5 5.283325
ENSG00000000419.11 1436.099009
ENSG00000000457.12 878.159905
ENSG00000000460.15 495.546941
ENSG00000000938.11 358.845115
treatedF_28ef84e7-f566-40a7-b239-26d3e23c878a.htseq.counts
ENSG00000000003.13 6656.17608
ENSG00000000005.5 6.66918
ENSG00000000419.11 1812.79828
ENSG00000000457.12 1108.50767
ENSG00000000460.15 625.53253
ENSG00000000938.11 452.97281
treatedF_2baabd07-b92c-4ac1-8de7-3d8df4f4a80b.htseq.counts
ENSG00000000003.13 7094.851646
ENSG00000000005.5 7.108713
ENSG00000000419.11 1932.270827
ENSG00000000457.12 1181.563914
ENSG00000000460.15 666.758275
ENSG00000000938.11 482.826005
treatedF_3e0831c0-6726-4f71-9cba-faaeea280cf9.htseq.counts
ENSG00000000003.13 5619.53140
ENSG00000000005.5 5.63051
ENSG00000000419.11 1530.46986
ENSG00000000457.12 935.86672
ENSG00000000460.15 528.11098
ENSG00000000938.11 382.42602
treatedF_554f6de3-63c7-47b1-a75a-dcfc73f54e96.htseq.counts
ENSG00000000003.13 4540.472811
ENSG00000000005.5 4.549344
ENSG00000000419.11 1236.590079
ENSG00000000457.12 756.162228
ENSG00000000460.15 426.703470
ENSG00000000938.11 308.992839
treatedF_6cd9b90b-0c6c-44bd-8536-5a93553a7730.htseq.counts
ENSG00000000003.13 3160.483427
ENSG00000000005.5 3.166658
ENSG00000000419.11 860.752308
ENSG00000000457.12 526.341262
ENSG00000000460.15 297.015157
ENSG00000000938.11 215.080408
treatedF_7a3a131b-883d-4f82-8b3b-ede7733f68d8.htseq.counts
ENSG00000000003.13 4584.545402
ENSG00000000005.5 4.593502
ENSG00000000419.11 1248.593174
ENSG00000000457.12 763.501998
ENSG00000000460.15 430.845314
ENSG00000000938.11 311.992111
treatedF_7b77e8cb-3f1d-4af7-b609-d75f912484c4.htseq.counts
ENSG00000000003.13 6597.84003
ENSG00000000005.5 6.61073
ENSG00000000419.11 1796.91056
ENSG00000000457.12 1098.79249
ENSG00000000460.15 620.05024
ENSG00000000938.11 449.00287
treatedF_89e20bd9-15e5-48e6-9dfe-0b919c817216.htseq.counts
ENSG00000000003.13 4677.991367
ENSG00000000005.5 4.687131
ENSG00000000419.11 1274.043024
ENSG00000000457.12 779.064322
ENSG00000000460.15 439.627156
ENSG00000000938.11 318.351390
treatedF_98380eb7-4de1-4e3a-989c-eedf6eec2977.htseq.counts
ENSG00000000003.13 4015.830234
ENSG00000000005.5 4.023676
ENSG00000000419.11 1093.704562
ENSG00000000457.12 668.789191
ENSG00000000460.15 377.398736
ENSG00000000938.11 273.289332
treatedF_9ccd91ba-7180-443a-b03b-f9b398c679e4.htseq.counts
ENSG00000000003.13 2103.303007
ENSG00000000005.5 2.107412
ENSG00000000419.11 572.831011
ENSG00000000457.12 350.280324
ENSG00000000460.15 197.663708
ENSG00000000938.11 143.136099
treatedF_aaec3912-230f-4418-986d-878e77480f94.htseq.counts
ENSG00000000003.13 3934.649572
ENSG00000000005.5 3.942337
ENSG00000000419.11 1071.595146
ENSG00000000457.12 655.269508
ENSG00000000460.15 369.769559
ENSG00000000938.11 267.764744
treatedF_d5fd715a-cf6d-4b29-ad9d-b3e58c55262a.htseq.counts
ENSG00000000003.13 4680.411947
ENSG00000000005.5 4.689556
ENSG00000000419.11 1274.702265
ENSG00000000457.12 779.467442
ENSG00000000460.15 439.854637
ENSG00000000938.11 318.516118
treatedF_ee857c4c-e6a9-4f39-b95b-20fe46dd1ab7.htseq.counts
ENSG00000000003.13 3216.739634
ENSG00000000005.5 3.223024
ENSG00000000419.11 876.073590
ENSG00000000457.12 535.710070
ENSG00000000460.15 302.301990
ENSG00000000938.11 218.908812
treatedF_eea3fcee-ee51-461b-abb4-c393c084e018.htseq.counts
ENSG00000000003.13 3626.52501
ENSG00000000005.5 3.63361
ENSG00000000419.11 987.67794
ENSG00000000457.12 603.95499
ENSG00000000460.15 340.81270
ENSG00000000938.11 246.79594
treatedF_f6ae6ac1-3e00-4021-a6e7-fbb0d5f12836.htseq.counts
ENSG00000000003.13 5969.399371
ENSG00000000005.5 5.981062
ENSG00000000419.11 1625.755807
ENSG00000000457.12 994.133104
ENSG00000000460.15 560.990790
ENSG00000000938.11 406.235591
treatedM_04e7f1a4-3173-4a6f-af60-04e1f2e29868.htseq.counts
ENSG00000000003.13 5156.248498
ENSG00000000005.5 5.166322
ENSG00000000419.11 1404.295544
ENSG00000000457.12 858.712410
ENSG00000000460.15 484.572691
ENSG00000000938.11 350.898227
treatedM_05ac7b05-e459-4833-97fc-530185a7a55f.htseq.counts
ENSG00000000003.13 2360.802120
ENSG00000000005.5 2.365414
ENSG00000000419.11 642.960458
ENSG00000000457.12 393.163766
ENSG00000000460.15 221.862898
ENSG00000000938.11 160.659689
treatedM_063411ca-874c-49ff-85c2-b6946f43df4e.htseq.counts
ENSG00000000003.13 7355.353250
ENSG00000000005.5 7.369723
ENSG00000000419.11 2003.217998
ENSG00000000457.12 1224.947386
ENSG00000000460.15 691.239633
ENSG00000000938.11 500.553923
treatedM_1c6bb58a-3869-41f5-9fef-9070bbfedbad.htseq.counts
ENSG00000000003.13 4271.120665
ENSG00000000005.5 4.279465
ENSG00000000419.11 1163.232478
ENSG00000000457.12 711.304803
ENSG00000000460.15 401.390359
ENSG00000000938.11 290.662614
treatedM_51c2d807-7ee6-4b42-a6a7-3eb14f987bc0.htseq.counts
ENSG00000000003.13 3490.883259
ENSG00000000005.5 3.497703
ENSG00000000419.11 950.736142
ENSG00000000457.12 581.365460
ENSG00000000460.15 328.065394
ENSG00000000938.11 237.565111
treatedM_57ef7745-338c-4fb2-ac9b-9f57daba2c51.htseq.counts
ENSG00000000003.13 2958.87940
ENSG00000000005.5 2.96466
ENSG00000000419.11 805.84579
ENSG00000000457.12 492.76649
ENSG00000000460.15 278.06886
ENSG00000000938.11 201.36065
treatedM_77b9a94e-aaa7-409c-9849-86ba7d5c061a.htseq.counts
ENSG00000000003.13 4764.475611
ENSG00000000005.5 4.773784
ENSG00000000419.11 1297.596862
ENSG00000000457.12 793.467254
ENSG00000000460.15 447.754752
ENSG00000000938.11 324.236903
treatedM_79f4b12a-ed1c-46d5-ae3d-a0422454eaf4.htseq.counts
ENSG00000000003.13 4890.222459
ENSG00000000005.5 4.899776
ENSG00000000419.11 1331.843803
ENSG00000000457.12 814.408909
ENSG00000000460.15 459.572159
ENSG00000000938.11 332.794355
treatedM_7f86ace4-9a17-4b17-8a79-3b2ef53f62c3.htseq.counts
ENSG00000000003.13 2043.549470
ENSG00000000005.5 2.047542
ENSG00000000419.11 556.557236
ENSG00000000457.12 340.329077
ENSG00000000460.15 192.048205
ENSG00000000938.11 139.069691
treatedM_9700948e-21f5-42ae-9cb5-f18c745887ce.htseq.counts
ENSG00000000003.13 3186.161218
ENSG00000000005.5 3.192386
ENSG00000000419.11 867.745610
ENSG00000000457.12 530.617595
ENSG00000000460.15 299.428299
ENSG00000000938.11 216.827859
treatedM_a3a6543b-ea79-4724-a140-c83392b1842b.htseq.counts
ENSG00000000003.13 2997.201091
ENSG00000000005.5 3.003057
ENSG00000000419.11 816.282640
ENSG00000000457.12 499.148513
ENSG00000000460.15 281.670249
ENSG00000000938.11 203.968554
treatedM_b5d92dd1-d98b-4b9e-953e-81c04dfb1e0d.htseq.counts
ENSG00000000003.13 6931.404510
ENSG00000000005.5 6.944946
ENSG00000000419.11 1887.756277
ENSG00000000457.12 1154.343720
ENSG00000000460.15 651.397879
ENSG00000000938.11 471.702936
treatedM_bdd35388-0850-40ac-a21a-6bfee0c34eef.htseq.counts
ENSG00000000003.13 4658.579772
ENSG00000000005.5 4.667681
ENSG00000000419.11 1268.756309
ENSG00000000457.12 775.831550
ENSG00000000460.15 437.802898
ENSG00000000938.11 317.030373
treatedM_c49c187f-98e7-463d-a18b-accf3205eb81.htseq.counts
ENSG00000000003.13 3603.133030
ENSG00000000005.5 3.610172
ENSG00000000419.11 981.307177
ENSG00000000457.12 600.059336
ENSG00000000460.15 338.614376
ENSG00000000938.11 245.204046
treatedM_c4c4578a-f1c2-462a-873f-c8db84fe3a6f.htseq.counts
ENSG00000000003.13 3315.768855
ENSG00000000005.5 3.322247
ENSG00000000419.11 903.044031
ENSG00000000457.12 552.202220
ENSG00000000460.15 311.608534
ENSG00000000938.11 225.648049
treatedM_c7e1465f-cc5a-4dc9-9bb1-6f1112da7aad.htseq.counts
ENSG00000000003.13 5592.198160
ENSG00000000005.5 5.603124
ENSG00000000419.11 1523.025696
ENSG00000000457.12 931.314688
ENSG00000000460.15 525.542264
ENSG00000000938.11 380.565914
treatedM_dad3353e-6721-4e2e-ae06-04eea4c00f12.htseq.counts
ENSG00000000003.13 5816.058357
ENSG00000000005.5 5.827421
ENSG00000000419.11 1583.993641
ENSG00000000457.12 968.595965
ENSG00000000460.15 546.580145
ENSG00000000938.11 395.800274
treatedM_dcf5a350-7cff-475a-8f53-376422f990eb.htseq.counts
ENSG00000000003.13 4039.896492
ENSG00000000005.5 4.047789
ENSG00000000419.11 1100.258966
ENSG00000000457.12 672.797142
ENSG00000000460.15 379.660429
ENSG00000000938.11 274.927114
treatedM_e48c520a-d62c-440d-b17c-5b5ff03d41a2.htseq.counts
ENSG00000000003.13 4338.526111
ENSG00000000005.5 4.347002
ENSG00000000419.11 1181.590237
ENSG00000000457.12 722.530385
ENSG00000000460.15 407.724972
ENSG00000000938.11 295.249758
treatedM_e4d48564-e021-4bbc-bc00-145e9d64b501.htseq.counts
ENSG00000000003.13 5336.018150
ENSG00000000005.5 5.346443
ENSG00000000419.11 1453.255504
ENSG00000000457.12 888.650927
ENSG00000000460.15 501.467040
ENSG00000000938.11 363.132093
untreatedF_0d9e4b58-c22f-4de0-8b0d-0b5a8e19a1af.htseq.counts
ENSG00000000003.13 4504.349177
ENSG00000000005.5 4.337283
ENSG00000000419.11 1135.530590
ENSG00000000457.12 651.582832
ENSG00000000460.15 277.800400
ENSG00000000938.11 248.635727
untreatedF_104c7c7e-583a-4496-a685-5d277e28c11b.htseq.counts
ENSG00000000003.13 5607.215962
ENSG00000000005.5 5.399244
ENSG00000000419.11 1413.559429
ENSG00000000457.12 811.119545
ENSG00000000460.15 345.818403
ENSG00000000938.11 309.512909
untreatedF_10a32136-8a4d-4af3-8e70-543b2a336c91.htseq.counts
ENSG00000000003.13 2929.506533
ENSG00000000005.5 2.820851
ENSG00000000419.11 738.518297
ENSG00000000457.12 423.771801
ENSG00000000460.15 180.673846
ENSG00000000938.11 161.705933
untreatedF_16fc8611-259d-4cd8-9e93-60d97bebb6bf.htseq.counts
ENSG00000000003.13 5900.424472
ENSG00000000005.5 5.681578
ENSG00000000419.11 1487.476264
ENSG00000000457.12 853.534026
ENSG00000000460.15 363.901691
ENSG00000000938.11 325.697736
untreatedF_21a0ef5f-24f5-45fe-ac84-deed4ef25329.htseq.counts
ENSG00000000003.13 6056.223056
ENSG00000000005.5 5.831598
ENSG00000000419.11 1526.752539
ENSG00000000457.12 876.071284
ENSG00000000460.15 373.510384
ENSG00000000938.11 334.297668
untreatedF_2f3f2e57-4c69-469f-be9c-01cc4f704427.htseq.counts
ENSG00000000003.13 3987.678514
ENSG00000000005.5 3.839775
ENSG00000000419.11 1005.279733
ENSG00000000457.12 576.843126
ENSG00000000460.15 245.935349
ENSG00000000938.11 220.116005
untreatedF_3e0831c0-6726-4f71-9cba-faaeea280cf9.htseq.counts
ENSG00000000003.13 6454.197647
ENSG00000000005.5 6.214811
ENSG00000000419.11 1627.080534
ENSG00000000457.12 933.640847
ENSG00000000460.15 398.054995
ENSG00000000938.11 356.265481
untreatedF_6c86f9ae-9e88-4eae-9ba3-4866943cca7f.htseq.counts
ENSG00000000003.13 5589.864468
ENSG00000000005.5 5.382536
ENSG00000000419.11 1409.185178
ENSG00000000457.12 808.609541
ENSG00000000460.15 344.748270
ENSG00000000938.11 308.555124
untreatedF_73756e81-79a2-4bff-96e7-99f038306b3e.htseq.counts
ENSG00000000003.13 6082.864700
ENSG00000000005.5 5.857251
ENSG00000000419.11 1533.468804
ENSG00000000457.12 879.925168
ENSG00000000460.15 375.153476
ENSG00000000938.11 335.768261
untreatedF_8d78e34d-490b-4f2e-ba1a-427afe96d26e.htseq.counts
ENSG00000000003.13 5324.701596
ENSG00000000005.5 5.127208
ENSG00000000419.11 1342.338551
ENSG00000000457.12 770.252040
ENSG00000000460.15 328.394664
ENSG00000000938.11 293.918389
untreatedF_92ee9ee1-8f03-4b53-b6c2-04d22fd692ae.htseq.counts
ENSG00000000003.13 4749.523958
ENSG00000000005.5 4.573364
ENSG00000000419.11 1197.338291
ENSG00000000457.12 687.048927
ENSG00000000460.15 292.921265
ENSG00000000938.11 262.169139
untreatedF_98380eb7-4de1-4e3a-989c-eedf6eec2977.htseq.counts
ENSG00000000003.13 4612.299530
ENSG00000000005.5 4.441229
ENSG00000000419.11 1162.744495
ENSG00000000457.12 667.198539
ENSG00000000460.15 284.458110
ENSG00000000938.11 254.594483
untreatedF_99e82612-a602-459b-8a60-80a812bf9d88.htseq.counts
ENSG00000000003.13 4374.358038
ENSG00000000005.5 4.212113
ENSG00000000419.11 1102.760281
ENSG00000000457.12 632.778785
ENSG00000000460.15 269.783351
ENSG00000000938.11 241.460342
untreatedF_b39bcb10-164d-48c5-89ba-9ef668765db6.htseq.counts
ENSG00000000003.13 4958.78099
ENSG00000000005.5 4.77486
ENSG00000000419.11 1250.09125
ENSG00000000457.12 717.31929
ENSG00000000460.15 305.82694
ENSG00000000938.11 273.71992
untreatedF_b49faa57-5a15-4193-9552-130d9a63eb40.htseq.counts
ENSG00000000003.13 9375.598888
ENSG00000000005.5 9.027858
ENSG00000000419.11 2363.555515
ENSG00000000457.12 1356.240165
ENSG00000000460.15 578.228956
ENSG00000000938.11 517.524010
untreatedF_d2bf6185-08a5-4a73-9f87-7164cca1ccf6.htseq.counts
ENSG00000000003.13 1650.499750
ENSG00000000005.5 1.589283
ENSG00000000419.11 416.085184
ENSG00000000457.12 238.755314
ENSG00000000460.15 101.792617
ENSG00000000938.11 91.105993
untreatedF_edf02d6d-619f-4325-a585-dca7bf5afbeb.htseq.counts
ENSG00000000003.13 2872.655275
ENSG00000000005.5 2.766108
ENSG00000000419.11 724.186295
ENSG00000000457.12 415.547904
ENSG00000000460.15 177.167612
ENSG00000000938.11 158.567799
untreatedF_eed21a5a-30db-45a0-9b60-3f6a91b38cb6.htseq.counts
ENSG00000000003.13 7821.524199
ENSG00000000005.5 7.531424
ENSG00000000419.11 1971.778750
ENSG00000000457.12 1131.433352
ENSG00000000460.15 482.383241
ENSG00000000938.11 431.740587
untreatedF_f7a956f8-4dc2-437a-92db-8baf8f9b3f14.htseq.counts
ENSG00000000003.13 6584.478980
ENSG00000000005.5 6.340261
ENSG00000000419.11 1659.924000
ENSG00000000457.12 952.486872
ENSG00000000460.15 406.089942
ENSG00000000938.11 363.456885
untreatedF_ffeed225-c2a3-4b4c-954c-4816903782a9.htseq.counts
ENSG00000000003.13 7106.384594
ENSG00000000005.5 6.842809
ENSG00000000419.11 1791.494570
ENSG00000000457.12 1027.983847
ENSG00000000460.15 438.277853
ENSG00000000938.11 392.265571
untreatedM_09f395dd-d007-41e0-8a51-a6533ae51087.htseq.counts
ENSG00000000003.13 4440.766989
ENSG00000000005.5 4.276059
ENSG00000000419.11 1119.501744
ENSG00000000457.12 642.385263
ENSG00000000460.15 273.879044
ENSG00000000938.11 245.126052
untreatedM_10d6deec-fd89-4115-92f5-c9def40428b5.htseq.counts
ENSG00000000003.13 4981.548721
ENSG00000000005.5 4.796783
ENSG00000000419.11 1255.830917
ENSG00000000457.12 720.612789
ENSG00000000460.15 307.231117
ENSG00000000938.11 274.976681
untreatedM_1d782a72-61f3-4002-bee5-67daeb8244e3.htseq.counts
ENSG00000000003.13 3461.264997
ENSG00000000005.5 3.332887
ENSG00000000419.11 872.572736
ENSG00000000457.12 500.694053
ENSG00000000460.15 213.469419
ENSG00000000938.11 191.058487
untreatedM_2cc2e3ce-68cd-4690-9fff-5ecf86c2f57a.htseq.counts
ENSG00000000003.13 3866.885923
ENSG00000000005.5 3.723463
ENSG00000000419.11 974.828345
ENSG00000000457.12 559.369707
ENSG00000000460.15 238.485609
ENSG00000000938.11 213.448371
untreatedM_35a2858e-9787-457c-9435-33bd62332aa3.htseq.counts
ENSG00000000003.13 5551.613004
ENSG00000000005.5 5.345704
ENSG00000000419.11 1399.542119
ENSG00000000457.12 803.076222
ENSG00000000460.15 342.389156
ENSG00000000938.11 306.443680
untreatedM_78e27399-eb4a-4b86-992e-3e052bad044c.htseq.counts
ENSG00000000003.13 5620.875187
ENSG00000000005.5 5.412397
ENSG00000000419.11 1417.002872
ENSG00000000457.12 813.095439
ENSG00000000460.15 346.660820
ENSG00000000938.11 310.266885
untreatedM_89eb1fc8-6b38-446e-a4b0-fb9c520298dc.htseq.counts
ENSG00000000003.13 4739.302223
ENSG00000000005.5 4.563521
ENSG00000000419.11 1194.761427
ENSG00000000457.12 685.570288
ENSG00000000460.15 292.290851
ENSG00000000938.11 261.604909
untreatedM_9700948e-21f5-42ae-9cb5-f18c745887ce.htseq.counts
ENSG00000000003.13 3659.400181
ENSG00000000005.5 3.523673
ENSG00000000419.11 922.521919
ENSG00000000457.12 529.355571
ENSG00000000460.15 225.689172
ENSG00000000938.11 201.995358
untreatedM_a3a6543b-ea79-4724-a140-c83392b1842b.htseq.counts
ENSG00000000003.13 3442.373899
ENSG00000000005.5 3.314696
ENSG00000000419.11 867.810357
ENSG00000000457.12 497.961336
ENSG00000000460.15 212.304333
ENSG00000000938.11 190.015717
untreatedM_ad69efb1-61ab-4492-8468-9006dd00e915.htseq.counts
ENSG00000000003.13 5915.867879
ENSG00000000005.5 5.696448
ENSG00000000419.11 1491.369492
ENSG00000000457.12 855.768013
ENSG00000000460.15 364.854144
ENSG00000000938.11 326.550197
untreatedM_b04fb368-4b93-4ef9-ae9f-020484c1686b.htseq.counts
ENSG00000000003.13 5619.750386
ENSG00000000005.5 5.411314
ENSG00000000419.11 1416.719313
ENSG00000000457.12 812.932729
ENSG00000000460.15 346.591449
ENSG00000000938.11 310.204797
untreatedM_b1820867-e6b2-4228-ad00-19d1d7fddf67.htseq.counts
ENSG00000000003.13 4647.045287
ENSG00000000005.5 4.474686
ENSG00000000419.11 1171.503778
ENSG00000000457.12 672.224734
ENSG00000000460.15 286.601014
ENSG00000000938.11 256.512415
untreatedM_bdd35388-0850-40ac-a21a-6bfee0c34eef.htseq.counts
ENSG00000000003.13 5350.516342
ENSG00000000005.5 5.152066
ENSG00000000419.11 1348.846357
ENSG00000000457.12 773.986308
ENSG00000000460.15 329.986758
ENSG00000000938.11 295.343338
untreatedM_cfb40dba-37a7-4ae7-a2c9-34becc30f939.htseq.counts
ENSG00000000003.13 4096.716359
ENSG00000000005.5 3.944769
ENSG00000000419.11 1032.767790
ENSG00000000457.12 592.616145
ENSG00000000460.15 252.660129
ENSG00000000938.11 226.134789
untreatedM_d1cbb686-93d8-4349-8bf5-756887c60ebc.htseq.counts
ENSG00000000003.13 4659.690122
ENSG00000000005.5 4.486862
ENSG00000000419.11 1174.691496
ENSG00000000457.12 674.053890
ENSG00000000460.15 287.380869
ENSG00000000938.11 257.210397
untreatedM_d7a9f4a9-6998-45dc-9bc4-06f3f7110429.htseq.counts
ENSG00000000003.13 4740.739575
ENSG00000000005.5 4.564906
ENSG00000000419.11 1195.123778
ENSG00000000457.12 685.778210
ENSG00000000460.15 292.379498
ENSG00000000938.11 261.684249
untreatedM_e035a46e-6114-4a64-b5ae-9e6209223493.htseq.counts
ENSG00000000003.13 5511.063043
ENSG00000000005.5 5.306658
ENSG00000000419.11 1389.319616
ENSG00000000457.12 797.210412
ENSG00000000460.15 339.888286
ENSG00000000938.11 304.205361
untreatedM_e208fa4d-3f65-4615-bd6e-870a52bb6da3.htseq.counts
ENSG00000000003.13 6466.898511
ENSG00000000005.5 6.227041
ENSG00000000419.11 1630.282377
ENSG00000000457.12 935.478108
ENSG00000000460.15 398.838306
ENSG00000000938.11 356.966556
untreatedM_fbbb6d26-8bd4-40da-870b-d8db0f653cfa.htseq.counts
ENSG00000000003.13 1936.565431
ENSG00000000005.5 1.864738
ENSG00000000419.11 488.201336
ENSG00000000457.12 280.136539
ENSG00000000460.15 119.435379
ENSG00000000938.11 106.896543
untreatedM_fe76a5ca-f70a-4ab7-b080-5a19ae36dc2b.htseq.counts
ENSG00000000003.13 3112.455176
ENSG00000000005.5 2.997014
ENSG00000000419.11 784.639007
ENSG00000000457.12 450.236489
ENSG00000000460.15 191.956986
ENSG00000000938.11 171.804522
head(assays(dds)[["cooks"]])
treatedF_004c60cf-c08e-49df-b4ce-baca41e11250.htseq.counts
ENSG00000000003.13 5.097136e-06
ENSG00000000005.5 4.540728e-03
ENSG00000000419.11 2.339074e-02
ENSG00000000457.12 3.270106e-02
ENSG00000000460.15 2.824245e-02
ENSG00000000938.11 2.073188e-02
treatedF_0d9e4b58-c22f-4de0-8b0d-0b5a8e19a1af.htseq.counts
ENSG00000000003.13 1.511184e-05
ENSG00000000005.5 5.429639e-03
ENSG00000000419.11 1.060596e-03
ENSG00000000457.12 1.681533e-02
ENSG00000000460.15 2.704269e-02
ENSG00000000938.11 1.645325e-03
treatedF_160aee04-df36-4e94-90c5-b01b2991ba48.htseq.counts
ENSG00000000003.13 0.0003694600
ENSG00000000005.5 0.0065179702
ENSG00000000419.11 0.0006164506
ENSG00000000457.12 0.0003061180
ENSG00000000460.15 0.0314551615
ENSG00000000938.11 0.0024000702
treatedF_1a228668-b2a0-469f-8801-fdc8be449b44.htseq.counts
ENSG00000000003.13 0.0003266357
ENSG00000000005.5 0.0238143309
ENSG00000000419.11 0.0052478592
ENSG00000000457.12 0.0243284585
ENSG00000000460.15 0.0005685959
ENSG00000000938.11 0.0063354828
treatedF_21a0ef5f-24f5-45fe-ac84-deed4ef25329.htseq.counts
ENSG00000000003.13 0.008548513
ENSG00000000005.5 0.025982939
ENSG00000000419.11 0.003617809
ENSG00000000457.12 0.002604817
ENSG00000000460.15 0.001545922
ENSG00000000938.11 0.010297829
treatedF_28ef84e7-f566-40a7-b239-26d3e23c878a.htseq.counts
ENSG00000000003.13 0.038444149
ENSG00000000005.5 0.013991799
ENSG00000000419.11 0.008067015
ENSG00000000457.12 0.015691953
ENSG00000000460.15 0.028631791
ENSG00000000938.11 0.114351840
treatedF_2baabd07-b92c-4ac1-8de7-3d8df4f4a80b.htseq.counts
ENSG00000000003.13 0.014681702
ENSG00000000005.5 0.009759370
ENSG00000000419.11 0.001360615
ENSG00000000457.12 0.030812701
ENSG00000000460.15 0.196656249
ENSG00000000938.11 0.003538153
treatedF_3e0831c0-6726-4f71-9cba-faaeea280cf9.htseq.counts
ENSG00000000003.13 0.0076365755
ENSG00000000005.5 0.0111009122
ENSG00000000419.11 0.0284720514
ENSG00000000457.12 0.0050802522
ENSG00000000460.15 0.0001723787
ENSG00000000938.11 0.2462321206
treatedF_554f6de3-63c7-47b1-a75a-dcfc73f54e96.htseq.counts
ENSG00000000003.13 0.002525971
ENSG00000000005.5 0.024254704
ENSG00000000419.11 0.368995380
ENSG00000000457.12 0.020506818
ENSG00000000460.15 0.009793162
ENSG00000000938.11 0.098957636
treatedF_6cd9b90b-0c6c-44bd-8536-5a93553a7730.htseq.counts
ENSG00000000003.13 0.0106473831
ENSG00000000005.5 0.0291974706
ENSG00000000419.11 0.0132479102
ENSG00000000457.12 0.0003412658
ENSG00000000460.15 0.0263022772
ENSG00000000938.11 0.0117082156
treatedF_7a3a131b-883d-4f82-8b3b-ede7733f68d8.htseq.counts
ENSG00000000003.13 3.948808e-06
ENSG00000000005.5 7.767884e-03
ENSG00000000419.11 7.557361e-03
ENSG00000000457.12 5.833968e-04
ENSG00000000460.15 2.016568e-02
ENSG00000000938.11 2.096087e-02
treatedF_7b77e8cb-3f1d-4af7-b609-d75f912484c4.htseq.counts
ENSG00000000003.13 0.0295731004
ENSG00000000005.5 0.0284520336
ENSG00000000419.11 0.0106571545
ENSG00000000457.12 0.0319810916
ENSG00000000460.15 0.0001320881
ENSG00000000938.11 0.0020804718
treatedF_89e20bd9-15e5-48e6-9dfe-0b919c817216.htseq.counts
ENSG00000000003.13 2.199209e-02
ENSG00000000005.5 2.460360e-02
ENSG00000000419.11 3.485329e-02
ENSG00000000457.12 2.790229e-05
ENSG00000000460.15 1.850636e-02
ENSG00000000938.11 2.890712e-03
treatedF_98380eb7-4de1-4e3a-989c-eedf6eec2977.htseq.counts
ENSG00000000003.13 1.198017e-04
ENSG00000000005.5 2.977119e+00
ENSG00000000419.11 2.174147e-06
ENSG00000000457.12 9.775186e-05
ENSG00000000460.15 2.672377e-02
ENSG00000000938.11 1.252959e-02
treatedF_9ccd91ba-7180-443a-b03b-f9b398c679e4.htseq.counts
ENSG00000000003.13 0.0002858424
ENSG00000000005.5 0.0121940009
ENSG00000000419.11 0.0026306094
ENSG00000000457.12 0.0229097153
ENSG00000000460.15 0.0131676638
ENSG00000000938.11 0.0102711102
treatedF_aaec3912-230f-4418-986d-878e77480f94.htseq.counts
ENSG00000000003.13 0.011983428
ENSG00000000005.5 0.013569947
ENSG00000000419.11 0.053027247
ENSG00000000457.12 0.003353263
ENSG00000000460.15 0.002565868
ENSG00000000938.11 0.009330105
treatedF_d5fd715a-cf6d-4b29-ad9d-b3e58c55262a.htseq.counts
ENSG00000000003.13 0.0024740134
ENSG00000000005.5 0.0246096284
ENSG00000000419.11 0.0050487511
ENSG00000000457.12 0.0009189565
ENSG00000000460.15 0.0002765465
ENSG00000000938.11 0.0036816752
treatedF_ee857c4c-e6a9-4f39-b95b-20fe46dd1ab7.htseq.counts
ENSG00000000003.13 6.062776e-05
ENSG00000000005.5 6.469538e-02
ENSG00000000419.11 1.155467e-03
ENSG00000000457.12 6.198118e-05
ENSG00000000460.15 8.161691e-05
ENSG00000000938.11 1.016986e-02
treatedF_eea3fcee-ee51-461b-abb4-c393c084e018.htseq.counts
ENSG00000000003.13 0.002096768
ENSG00000000005.5 0.003051693
ENSG00000000419.11 0.036213637
ENSG00000000457.12 0.005640711
ENSG00000000460.15 0.014680014
ENSG00000000938.11 0.006031034
treatedF_f6ae6ac1-3e00-4021-a6e7-fbb0d5f12836.htseq.counts
ENSG00000000003.13 0.0156436424
ENSG00000000005.5 0.0189827972
ENSG00000000419.11 0.0305338996
ENSG00000000457.12 0.0004083158
ENSG00000000460.15 0.0045101211
ENSG00000000938.11 0.0153672900
treatedM_04e7f1a4-3173-4a6f-af60-04e1f2e29868.htseq.counts
ENSG00000000003.13 6.870673e-03
ENSG00000000005.5 1.673185e-02
ENSG00000000419.11 1.278957e-03
ENSG00000000457.12 5.270714e-06
ENSG00000000460.15 2.382055e-04
ENSG00000000938.11 3.091657e-04
treatedM_05ac7b05-e459-4833-97fc-530185a7a55f.htseq.counts
ENSG00000000003.13 0.192866610
ENSG00000000005.5 0.005481857
ENSG00000000419.11 0.015823998
ENSG00000000457.12 0.032971961
ENSG00000000460.15 0.017033661
ENSG00000000938.11 0.002250537
treatedM_063411ca-874c-49ff-85c2-b6946f43df4e.htseq.counts
ENSG00000000003.13 0.100581268
ENSG00000000005.5 0.006185201
ENSG00000000419.11 0.144308511
ENSG00000000457.12 0.003757016
ENSG00000000460.15 0.029966974
ENSG00000000938.11 0.002859054
treatedM_1c6bb58a-3869-41f5-9fef-9070bbfedbad.htseq.counts
ENSG00000000003.13 0.0190103793
ENSG00000000005.5 0.0001003638
ENSG00000000419.11 0.0016601359
ENSG00000000457.12 0.0005791009
ENSG00000000460.15 0.0058002730
ENSG00000000938.11 0.0353449192
treatedM_51c2d807-7ee6-4b42-a6a7-3eb14f987bc0.htseq.counts
ENSG00000000003.13 0.0034551553
ENSG00000000005.5 0.0211223018
ENSG00000000419.11 0.0154144936
ENSG00000000457.12 0.0025017237
ENSG00000000460.15 0.0000161509
ENSG00000000938.11 0.0041627244
treatedM_57ef7745-338c-4fb2-ac9b-9f57daba2c51.htseq.counts
ENSG00000000003.13 3.838229e-02
ENSG00000000005.5 3.544631e-02
ENSG00000000419.11 1.693698e-06
ENSG00000000457.12 1.048623e-02
ENSG00000000460.15 6.843557e-02
ENSG00000000938.11 1.152993e-02
treatedM_77b9a94e-aaa7-409c-9849-86ba7d5c061a.htseq.counts
ENSG00000000003.13 0.008492739
ENSG00000000005.5 0.024816856
ENSG00000000419.11 0.014502805
ENSG00000000457.12 0.010295546
ENSG00000000460.15 0.016814097
ENSG00000000938.11 0.003697086
treatedM_79f4b12a-ed1c-46d5-ae3d-a0422454eaf4.htseq.counts
ENSG00000000003.13 1.026927e-02
ENSG00000000005.5 1.591205e-02
ENSG00000000419.11 4.687189e-03
ENSG00000000457.12 4.541374e-07
ENSG00000000460.15 2.518872e-03
ENSG00000000938.11 5.980860e-03
treatedM_7f86ace4-9a17-4b17-8a79-3b2ef53f62c3.htseq.counts
ENSG00000000003.13 0.009588653
ENSG00000000005.5 0.003871843
ENSG00000000419.11 0.013613150
ENSG00000000457.12 0.001735624
ENSG00000000460.15 0.037790013
ENSG00000000938.11 0.020908866
treatedM_9700948e-21f5-42ae-9cb5-f18c745887ce.htseq.counts
ENSG00000000003.13 0.006972302
ENSG00000000005.5 0.020022171
ENSG00000000419.11 0.009419123
ENSG00000000457.12 0.017296544
ENSG00000000460.15 0.015040745
ENSG00000000938.11 0.011337716
treatedM_a3a6543b-ea79-4724-a140-c83392b1842b.htseq.counts
ENSG00000000003.13 5.575653e-04
ENSG00000000005.5 8.580543e-03
ENSG00000000419.11 1.631930e-03
ENSG00000000457.12 1.723261e-02
ENSG00000000460.15 2.184944e-02
ENSG00000000938.11 6.469058e-06
treatedM_b5d92dd1-d98b-4b9e-953e-81c04dfb1e0d.htseq.counts
ENSG00000000003.13 0.0031957549
ENSG00000000005.5 0.0289717456
ENSG00000000419.11 0.0001130022
ENSG00000000457.12 0.0184028492
ENSG00000000460.15 0.5309545497
ENSG00000000938.11 0.0152771353
treatedM_bdd35388-0850-40ac-a21a-6bfee0c34eef.htseq.counts
ENSG00000000003.13 2.529449e-03
ENSG00000000005.5 1.244655e-04
ENSG00000000419.11 2.418367e-03
ENSG00000000457.12 6.624570e-07
ENSG00000000460.15 1.193138e-02
ENSG00000000938.11 7.146091e-03
treatedM_c49c187f-98e7-463d-a18b-accf3205eb81.htseq.counts
ENSG00000000003.13 0.006119266
ENSG00000000005.5 0.116131537
ENSG00000000419.11 0.000943359
ENSG00000000457.12 0.003409753
ENSG00000000460.15 0.021343084
ENSG00000000938.11 0.006487061
treatedM_c4c4578a-f1c2-462a-873f-c8db84fe3a6f.htseq.counts
ENSG00000000003.13 0.005095565
ENSG00000000005.5 0.003247638
ENSG00000000419.11 0.003039194
ENSG00000000457.12 0.013984406
ENSG00000000460.15 0.018450754
ENSG00000000938.11 0.005272462
treatedM_c7e1465f-cc5a-4dc9-9bb1-6f1112da7aad.htseq.counts
ENSG00000000003.13 0.006509720
ENSG00000000005.5 0.046437310
ENSG00000000419.11 0.014094488
ENSG00000000457.12 0.008642259
ENSG00000000460.15 0.013154302
ENSG00000000938.11 0.013754629
treatedM_dad3353e-6721-4e2e-ae06-04eea4c00f12.htseq.counts
ENSG00000000003.13 4.626449e-03
ENSG00000000005.5 1.168301e-02
ENSG00000000419.11 1.385398e-05
ENSG00000000457.12 3.303839e-02
ENSG00000000460.15 1.011274e-02
ENSG00000000938.11 1.514369e-02
treatedM_dcf5a350-7cff-475a-8f53-376422f990eb.htseq.counts
ENSG00000000003.13 0.0001031364
ENSG00000000005.5 0.0228732608
ENSG00000000419.11 0.0274181533
ENSG00000000457.12 0.0001068395
ENSG00000000460.15 0.0033405871
ENSG00000000938.11 0.0195321157
treatedM_e48c520a-d62c-440d-b17c-5b5ff03d41a2.htseq.counts
ENSG00000000003.13 0.4258410615
ENSG00000000005.5 0.0140616183
ENSG00000000419.11 0.0005312089
ENSG00000000457.12 0.0976748060
ENSG00000000460.15 2.0451344816
ENSG00000000938.11 0.0170024847
treatedM_e4d48564-e021-4bbc-bc00-145e9d64b501.htseq.counts
ENSG00000000003.13 0.0084229260
ENSG00000000005.5 0.0172612935
ENSG00000000419.11 0.0003677522
ENSG00000000457.12 0.0014009858
ENSG00000000460.15 0.0098584068
ENSG00000000938.11 0.0083591585
untreatedF_0d9e4b58-c22f-4de0-8b0d-0b5a8e19a1af.htseq.counts
ENSG00000000003.13 0.001208439
ENSG00000000005.5 0.006843035
ENSG00000000419.11 0.003566997
ENSG00000000457.12 0.016689502
ENSG00000000460.15 0.021110996
ENSG00000000938.11 0.003150451
untreatedF_104c7c7e-583a-4496-a685-5d277e28c11b.htseq.counts
ENSG00000000003.13 4.454603e-05
ENSG00000000005.5 2.608687e-02
ENSG00000000419.11 2.288353e-01
ENSG00000000457.12 8.294396e-03
ENSG00000000460.15 2.909856e-02
ENSG00000000938.11 4.624667e-03
untreatedF_10a32136-8a4d-4af3-8e70-543b2a336c91.htseq.counts
ENSG00000000003.13 1.730598e-03
ENSG00000000005.5 1.843589e-02
ENSG00000000419.11 3.114133e-05
ENSG00000000457.12 2.647160e-03
ENSG00000000460.15 4.740210e-03
ENSG00000000938.11 1.165325e-01
untreatedF_16fc8611-259d-4cd8-9e93-60d97bebb6bf.htseq.counts
ENSG00000000003.13 0.0001758587
ENSG00000000005.5 0.0266560695
ENSG00000000419.11 0.0040837670
ENSG00000000457.12 0.0017847568
ENSG00000000460.15 0.0050409136
ENSG00000000938.11 0.0009593574
untreatedF_21a0ef5f-24f5-45fe-ac84-deed4ef25329.htseq.counts
ENSG00000000003.13 0.0125194575
ENSG00000000005.5 0.0269440370
ENSG00000000419.11 0.0007525892
ENSG00000000457.12 0.0027032236
ENSG00000000460.15 0.0155852901
ENSG00000000938.11 0.0092749039
untreatedF_2f3f2e57-4c69-469f-be9c-01cc4f704427.htseq.counts
ENSG00000000003.13 7.904144e-03
ENSG00000000005.5 3.851976e-05
ENSG00000000419.11 4.516748e-04
ENSG00000000457.12 1.436005e-01
ENSG00000000460.15 1.188869e-02
ENSG00000000938.11 7.486486e-05
untreatedF_3e0831c0-6726-4f71-9cba-faaeea280cf9.htseq.counts
ENSG00000000003.13 0.011551089
ENSG00000000005.5 0.012711766
ENSG00000000419.11 0.016796777
ENSG00000000457.12 0.005224965
ENSG00000000460.15 0.003064031
ENSG00000000938.11 0.297340049
untreatedF_6c86f9ae-9e88-4eae-9ba3-4866943cca7f.htseq.counts
ENSG00000000003.13 0.001188584
ENSG00000000005.5 0.026052011
ENSG00000000419.11 0.001076475
ENSG00000000457.12 0.008681698
ENSG00000000460.15 0.008663577
ENSG00000000938.11 0.007793832
untreatedF_73756e81-79a2-4bff-96e7-99f038306b3e.htseq.counts
ENSG00000000003.13 0.0031696581
ENSG00000000005.5 0.0064231702
ENSG00000000419.11 0.0006483591
ENSG00000000457.12 0.0035071075
ENSG00000000460.15 0.0001575320
ENSG00000000938.11 0.0013674522
untreatedF_8d78e34d-490b-4f2e-ba1a-427afe96d26e.htseq.counts
ENSG00000000003.13 0.002407762
ENSG00000000005.5 0.016524335
ENSG00000000419.11 0.041198086
ENSG00000000457.12 0.004112632
ENSG00000000460.15 0.005587493
ENSG00000000938.11 0.015502439
untreatedF_92ee9ee1-8f03-4b53-b6c2-04d22fd692ae.htseq.counts
ENSG00000000003.13 3.987154e-02
ENSG00000000005.5 2.084514e-01
ENSG00000000419.11 1.309392e-02
ENSG00000000457.12 6.392765e-05
ENSG00000000460.15 1.610602e-03
ENSG00000000938.11 1.682362e-02
untreatedF_98380eb7-4de1-4e3a-989c-eedf6eec2977.htseq.counts
ENSG00000000003.13 0.0004773145
ENSG00000000005.5 2.5089255138
ENSG00000000419.11 0.0007667327
ENSG00000000457.12 0.0001152018
ENSG00000000460.15 0.0207369696
ENSG00000000938.11 0.0115648919
untreatedF_99e82612-a602-459b-8a60-80a812bf9d88.htseq.counts
ENSG00000000003.13 1.237179e-02
ENSG00000000005.5 3.262195e-01
ENSG00000000419.11 1.511198e-05
ENSG00000000457.12 6.071959e-02
ENSG00000000460.15 1.479259e-04
ENSG00000000938.11 1.887587e-02
untreatedF_b39bcb10-164d-48c5-89ba-9ef668765db6.htseq.counts
ENSG00000000003.13 0.0214103299
ENSG00000000005.5 0.0112618735
ENSG00000000419.11 0.0005927917
ENSG00000000457.12 0.0001405413
ENSG00000000460.15 0.5010664551
ENSG00000000938.11 0.0049578850
untreatedF_b49faa57-5a15-4193-9552-130d9a63eb40.htseq.counts
ENSG00000000003.13 4.957875e-03
ENSG00000000005.5 3.139755e-02
ENSG00000000419.11 8.837287e-03
ENSG00000000457.12 4.572460e-03
ENSG00000000460.15 1.558606e-05
ENSG00000000938.11 2.926986e-03
untreatedF_d2bf6185-08a5-4a73-9f87-7164cca1ccf6.htseq.counts
ENSG00000000003.13 0.060345066
ENSG00000000005.5 0.001646551
ENSG00000000419.11 0.007439980
ENSG00000000457.12 0.009416688
ENSG00000000460.15 0.015894461
ENSG00000000938.11 0.012028953
untreatedF_edf02d6d-619f-4325-a585-dca7bf5afbeb.htseq.counts
ENSG00000000003.13 0.000687812
ENSG00000000005.5 0.018202933
ENSG00000000419.11 0.001088213
ENSG00000000457.12 0.315963472
ENSG00000000460.15 0.024198774
ENSG00000000938.11 0.016018744
untreatedF_eed21a5a-30db-45a0-9b60-3f6a91b38cb6.htseq.counts
ENSG00000000003.13 0.054843403
ENSG00000000005.5 0.029643682
ENSG00000000419.11 0.005202340
ENSG00000000457.12 0.009660807
ENSG00000000460.15 0.015159195
ENSG00000000938.11 0.001581403
untreatedF_f7a956f8-4dc2-437a-92db-8baf8f9b3f14.htseq.counts
ENSG00000000003.13 0.0057179754
ENSG00000000005.5 0.0278529562
ENSG00000000419.11 0.0271216272
ENSG00000000457.12 0.0018794787
ENSG00000000460.15 0.0076129307
ENSG00000000938.11 0.0005948193
untreatedF_ffeed225-c2a3-4b4c-954c-4816903782a9.htseq.counts
ENSG00000000003.13 5.469442e-03
ENSG00000000005.5 1.435516e-02
ENSG00000000419.11 4.186912e-04
ENSG00000000457.12 7.588330e-03
ENSG00000000460.15 3.551899e-05
ENSG00000000938.11 4.920432e-02
untreatedM_09f395dd-d007-41e0-8a51-a6533ae51087.htseq.counts
ENSG00000000003.13 4.693645e-02
ENSG00000000005.5 2.339752e-02
ENSG00000000419.11 4.018063e-05
ENSG00000000457.12 4.733184e-04
ENSG00000000460.15 4.404427e-03
ENSG00000000938.11 4.442557e-04
untreatedM_10d6deec-fd89-4115-92f5-c9def40428b5.htseq.counts
ENSG00000000003.13 1.441060e-02
ENSG00000000005.5 2.473801e-02
ENSG00000000419.11 1.281046e-05
ENSG00000000457.12 1.120623e-02
ENSG00000000460.15 4.122888e-03
ENSG00000000938.11 6.891180e-03
untreatedM_1d782a72-61f3-4002-bee5-67daeb8244e3.htseq.counts
ENSG00000000003.13 0.160847404
ENSG00000000005.5 0.451444319
ENSG00000000419.11 0.061652187
ENSG00000000457.12 0.028773478
ENSG00000000460.15 0.007672218
ENSG00000000938.11 0.001042582
untreatedM_2cc2e3ce-68cd-4690-9fff-5ecf86c2f57a.htseq.counts
ENSG00000000003.13 2.620074e-03
ENSG00000000005.5 8.308688e-02
ENSG00000000419.11 2.111761e-05
ENSG00000000457.12 1.605681e-02
ENSG00000000460.15 2.452265e-02
ENSG00000000938.11 1.939534e-02
untreatedM_35a2858e-9787-457c-9435-33bd62332aa3.htseq.counts
ENSG00000000003.13 0.0220960704
ENSG00000000005.5 0.0016460363
ENSG00000000419.11 0.0021284573
ENSG00000000457.12 0.0115394921
ENSG00000000460.15 0.1135153627
ENSG00000000938.11 0.0007718129
untreatedM_78e27399-eb4a-4b86-992e-3e052bad044c.htseq.counts
ENSG00000000003.13 0.0104068685
ENSG00000000005.5 0.0103804639
ENSG00000000419.11 0.0245228041
ENSG00000000457.12 0.0138241544
ENSG00000000460.15 0.0107621193
ENSG00000000938.11 0.0004033093
untreatedM_89eb1fc8-6b38-446e-a4b0-fb9c520298dc.htseq.counts
ENSG00000000003.13 0.0066492710
ENSG00000000005.5 0.0147315880
ENSG00000000419.11 0.0205066352
ENSG00000000457.12 0.0119442132
ENSG00000000460.15 0.0435840665
ENSG00000000938.11 0.0002820657
untreatedM_9700948e-21f5-42ae-9cb5-f18c745887ce.htseq.counts
ENSG00000000003.13 0.001708916
ENSG00000000005.5 0.021096633
ENSG00000000419.11 0.014484299
ENSG00000000457.12 0.017602073
ENSG00000000460.15 0.008098658
ENSG00000000938.11 0.010341625
untreatedM_a3a6543b-ea79-4724-a140-c83392b1842b.htseq.counts
ENSG00000000003.13 1.168041e-04
ENSG00000000005.5 9.930513e-03
ENSG00000000419.11 8.269681e-05
ENSG00000000457.12 1.710681e-02
ENSG00000000460.15 1.521302e-02
ENSG00000000938.11 2.338250e-04
untreatedM_ad69efb1-61ab-4492-8468-9006dd00e915.htseq.counts
ENSG00000000003.13 0.014465312
ENSG00000000005.5 0.026685048
ENSG00000000419.11 0.002618653
ENSG00000000457.12 0.013755412
ENSG00000000460.15 0.012753584
ENSG00000000938.11 0.012385014
untreatedM_b04fb368-4b93-4ef9-ae9f-020484c1686b.htseq.counts
ENSG00000000003.13 0.0017463807
ENSG00000000005.5 0.0261119653
ENSG00000000419.11 0.0261559899
ENSG00000000457.12 0.0276678233
ENSG00000000460.15 0.0017723731
ENSG00000000938.11 0.0009690299
untreatedM_b1820867-e6b2-4228-ad00-19d1d7fddf67.htseq.counts
ENSG00000000003.13 0.015978708
ENSG00000000005.5 0.000269299
ENSG00000000419.11 0.091488779
ENSG00000000457.12 0.007561010
ENSG00000000460.15 0.002490302
ENSG00000000938.11 0.004519391
untreatedM_bdd35388-0850-40ac-a21a-6bfee0c34eef.htseq.counts
ENSG00000000003.13 5.651200e-03
ENSG00000000005.5 2.226429e-05
ENSG00000000419.11 2.941987e-04
ENSG00000000457.12 3.721334e-11
ENSG00000000460.15 5.197749e-03
ENSG00000000938.11 6.103367e-03
untreatedM_cfb40dba-37a7-4ae7-a2c9-34becc30f939.htseq.counts
ENSG00000000003.13 3.711464e-03
ENSG00000000005.5 2.244358e-02
ENSG00000000419.11 3.545301e-02
ENSG00000000457.12 2.582771e-03
ENSG00000000460.15 1.216886e-02
ENSG00000000938.11 6.780245e-05
untreatedM_d1cbb686-93d8-4349-8bf5-756887c60ebc.htseq.counts
ENSG00000000003.13 0.018475412
ENSG00000000005.5 0.023961971
ENSG00000000419.11 0.017174311
ENSG00000000457.12 0.005037229
ENSG00000000460.15 0.001411792
ENSG00000000938.11 0.006864603
untreatedM_d7a9f4a9-6998-45dc-9bc4-06f3f7110429.htseq.counts
ENSG00000000003.13 0.0001141442
ENSG00000000005.5 0.0076284038
ENSG00000000419.11 0.0177618249
ENSG00000000457.12 0.0122297802
ENSG00000000460.15 0.0023923007
ENSG00000000938.11 0.0096337355
untreatedM_e035a46e-6114-4a64-b5ae-9e6209223493.htseq.counts
ENSG00000000003.13 0.002848487
ENSG00000000005.5 0.010053139
ENSG00000000419.11 0.002319246
ENSG00000000457.12 0.003839676
ENSG00000000460.15 0.009239785
ENSG00000000938.11 0.034473643
untreatedM_e208fa4d-3f65-4615-bd6e-870a52bb6da3.htseq.counts
ENSG00000000003.13 0.001014947
ENSG00000000005.5 0.019488890
ENSG00000000419.11 0.017584555
ENSG00000000457.12 0.005813947
ENSG00000000460.15 0.006449986
ENSG00000000938.11 0.015804211
untreatedM_fbbb6d26-8bd4-40da-870b-d8db0f653cfa.htseq.counts
ENSG00000000003.13 1.315399e-02
ENSG00000000005.5 7.195567e-05
ENSG00000000419.11 2.308053e-03
ENSG00000000457.12 7.209963e-02
ENSG00000000460.15 3.742431e-02
ENSG00000000938.11 8.734262e-03
untreatedM_fe76a5ca-f70a-4ab7-b080-5a19ae36dc2b.htseq.counts
ENSG00000000003.13 5.789846e-03
ENSG00000000005.5 1.901526e-08
ENSG00000000419.11 1.787723e-02
ENSG00000000457.12 1.235890e-02
ENSG00000000460.15 1.246501e-02
ENSG00000000938.11 3.538031e-03
head(dispersions(dds))
[1] 0.32867927 2.60374065 0.07648619 0.14699702 0.59314178 0.53329305
head(mcols(dds)$dispersion)
[1] 0.32867927 2.60374065 0.07648619 0.14699702 0.59314178 0.53329305
sizeFactors(dds)
treatedF_004c60cf-c08e-49df-b4ce-baca41e11250.htseq.counts
0.5246864
treatedF_0d9e4b58-c22f-4de0-8b0d-0b5a8e19a1af.htseq.counts
0.9459732
treatedF_160aee04-df36-4e94-90c5-b01b2991ba48.htseq.counts
0.7661427
treatedF_1a228668-b2a0-469f-8801-fdc8be449b44.htseq.counts
1.9999975
treatedF_21a0ef5f-24f5-45fe-ac84-deed4ef25329.htseq.counts
1.2718873
treatedF_28ef84e7-f566-40a7-b239-26d3e23c878a.htseq.counts
1.6055126
treatedF_2baabd07-b92c-4ac1-8de7-3d8df4f4a80b.htseq.counts
1.7113240
treatedF_3e0831c0-6726-4f71-9cba-faaeea280cf9.htseq.counts
1.3554672
treatedF_554f6de3-63c7-47b1-a75a-dcfc73f54e96.htseq.counts
1.0951914
treatedF_6cd9b90b-0c6c-44bd-8536-5a93553a7730.htseq.counts
0.7623290
treatedF_7a3a131b-883d-4f82-8b3b-ede7733f68d8.htseq.counts
1.1058219
treatedF_7b77e8cb-3f1d-4af7-b609-d75f912484c4.htseq.counts
1.5914416
treatedF_89e20bd9-15e5-48e6-9dfe-0b919c817216.htseq.counts
1.1283617
treatedF_98380eb7-4de1-4e3a-989c-eedf6eec2977.htseq.counts
0.9686442
treatedF_9ccd91ba-7180-443a-b03b-f9b398c679e4.htseq.counts
0.5073303
treatedF_aaec3912-230f-4418-986d-878e77480f94.htseq.counts
0.9490629
treatedF_d5fd715a-cf6d-4b29-ad9d-b3e58c55262a.htseq.counts
1.1289456
treatedF_ee857c4c-e6a9-4f39-b95b-20fe46dd1ab7.htseq.counts
0.7758984
treatedF_eea3fcee-ee51-461b-abb4-c393c084e018.htseq.counts
0.8747412
treatedF_f6ae6ac1-3e00-4021-a6e7-fbb0d5f12836.htseq.counts
1.4398577
treatedM_04e7f1a4-3173-4a6f-af60-04e1f2e29868.htseq.counts
1.2437204
treatedM_05ac7b05-e459-4833-97fc-530185a7a55f.htseq.counts
0.5694407
treatedM_063411ca-874c-49ff-85c2-b6946f43df4e.htseq.counts
1.7741587
treatedM_1c6bb58a-3869-41f5-9fef-9070bbfedbad.htseq.counts
1.0302219
treatedM_51c2d807-7ee6-4b42-a6a7-3eb14f987bc0.htseq.counts
0.8420236
treatedM_57ef7745-338c-4fb2-ac9b-9f57daba2c51.htseq.counts
0.7137008
treatedM_77b9a94e-aaa7-409c-9849-86ba7d5c061a.htseq.counts
1.1492223
treatedM_79f4b12a-ed1c-46d5-ae3d-a0422454eaf4.htseq.counts
1.1795532
treatedM_7f86ace4-9a17-4b17-8a79-3b2ef53f62c3.htseq.counts
0.4929173
treatedM_9700948e-21f5-42ae-9cb5-f18c745887ce.htseq.counts
0.7685227
treatedM_a3a6543b-ea79-4724-a140-c83392b1842b.htseq.counts
0.7229443
treatedM_b5d92dd1-d98b-4b9e-953e-81c04dfb1e0d.htseq.counts
1.6718995
treatedM_bdd35388-0850-40ac-a21a-6bfee0c34eef.htseq.counts
1.1236795
treatedM_c49c187f-98e7-463d-a18b-accf3205eb81.htseq.counts
0.8690989
treatedM_c4c4578a-f1c2-462a-873f-c8db84fe3a6f.htseq.counts
0.7997849
treatedM_c7e1465f-cc5a-4dc9-9bb1-6f1112da7aad.htseq.counts
1.3488743
treatedM_dad3353e-6721-4e2e-ae06-04eea4c00f12.htseq.counts
1.4028708
treatedM_dcf5a350-7cff-475a-8f53-376422f990eb.htseq.counts
0.9744491
treatedM_e48c520a-d62c-440d-b17c-5b5ff03d41a2.htseq.counts
1.0464805
treatedM_e4d48564-e021-4bbc-bc00-145e9d64b501.htseq.counts
1.2870820
untreatedF_0d9e4b58-c22f-4de0-8b0d-0b5a8e19a1af.htseq.counts
0.9459732
untreatedF_104c7c7e-583a-4496-a685-5d277e28c11b.htseq.counts
1.1775898
untreatedF_10a32136-8a4d-4af3-8e70-543b2a336c91.htseq.counts
0.6152353
untreatedF_16fc8611-259d-4cd8-9e93-60d97bebb6bf.htseq.counts
1.2391675
untreatedF_21a0ef5f-24f5-45fe-ac84-deed4ef25329.htseq.counts
1.2718873
untreatedF_2f3f2e57-4c69-469f-be9c-01cc4f704427.htseq.counts
0.8374655
untreatedF_3e0831c0-6726-4f71-9cba-faaeea280cf9.htseq.counts
1.3554672
untreatedF_6c86f9ae-9e88-4eae-9ba3-4866943cca7f.htseq.counts
1.1739458
untreatedF_73756e81-79a2-4bff-96e7-99f038306b3e.htseq.counts
1.2774824
untreatedF_8d78e34d-490b-4f2e-ba1a-427afe96d26e.htseq.counts
1.1182581
untreatedF_92ee9ee1-8f03-4b53-b6c2-04d22fd692ae.htseq.counts
0.9974631
untreatedF_98380eb7-4de1-4e3a-989c-eedf6eec2977.htseq.counts
0.9686442
untreatedF_99e82612-a602-459b-8a60-80a812bf9d88.htseq.counts
0.9186733
untreatedF_b39bcb10-164d-48c5-89ba-9ef668765db6.htseq.counts
1.0414099
untreatedF_b49faa57-5a15-4193-9552-130d9a63eb40.htseq.counts
1.9690003
untreatedF_d2bf6185-08a5-4a73-9f87-7164cca1ccf6.htseq.counts
0.3466269
untreatedF_edf02d6d-619f-4325-a585-dca7bf5afbeb.htseq.counts
0.6032958
untreatedF_eed21a5a-30db-45a0-9b60-3f6a91b38cb6.htseq.counts
1.6426240
untreatedF_f7a956f8-4dc2-437a-92db-8baf8f9b3f14.htseq.counts
1.3828281
untreatedF_ffeed225-c2a3-4b4c-954c-4816903782a9.htseq.counts
1.4924352
untreatedM_09f395dd-d007-41e0-8a51-a6533ae51087.htseq.counts
0.9326201
untreatedM_10d6deec-fd89-4115-92f5-c9def40428b5.htseq.counts
1.0461914
untreatedM_1d782a72-61f3-4002-bee5-67daeb8244e3.htseq.counts
0.7269116
untreatedM_2cc2e3ce-68cd-4690-9fff-5ecf86c2f57a.htseq.counts
0.8120974
untreatedM_35a2858e-9787-457c-9435-33bd62332aa3.htseq.counts
1.1659125
untreatedM_78e27399-eb4a-4b86-992e-3e052bad044c.htseq.counts
1.1804585
untreatedM_89eb1fc8-6b38-446e-a4b0-fb9c520298dc.htseq.counts
0.9953164
untreatedM_9700948e-21f5-42ae-9cb5-f18c745887ce.htseq.counts
0.7685227
untreatedM_a3a6543b-ea79-4724-a140-c83392b1842b.htseq.counts
0.7229443
untreatedM_ad69efb1-61ab-4492-8468-9006dd00e915.htseq.counts
1.2424108
untreatedM_b04fb368-4b93-4ef9-ae9f-020484c1686b.htseq.counts
1.1802222
untreatedM_b1820867-e6b2-4228-ad00-19d1d7fddf67.htseq.counts
0.9759412
untreatedM_bdd35388-0850-40ac-a21a-6bfee0c34eef.htseq.counts
1.1236795
untreatedM_cfb40dba-37a7-4ae7-a2c9-34becc30f939.htseq.counts
0.8603649
untreatedM_d1cbb686-93d8-4349-8bf5-756887c60ebc.htseq.counts
0.9785968
untreatedM_d7a9f4a9-6998-45dc-9bc4-06f3f7110429.htseq.counts
0.9956183
untreatedM_e035a46e-6114-4a64-b5ae-9e6209223493.htseq.counts
1.1573965
untreatedM_e208fa4d-3f65-4615-bd6e-870a52bb6da3.htseq.counts
1.3581346
untreatedM_fbbb6d26-8bd4-40da-870b-d8db0f653cfa.htseq.counts
0.4067045
untreatedM_fe76a5ca-f70a-4ab7-b080-5a19ae36dc2b.htseq.counts
0.6536569
head(coef(dds))
Intercept condition_treated_vs_untreated
ENSG00000000003.13 12.217232 -0.199787925
ENSG00000000005.5 2.196920 -0.142444941
ENSG00000000419.11 10.229280 -0.088311028
ENSG00000000457.12 9.427934 0.003435401
ENSG00000000460.15 8.198034 0.407873374
ENSG00000000938.11 8.038019 0.102227993
attr(dds, "betaPriorVar")
[1] 1e+06 1e+06
priorInfo(resLFC)
$type
[1] "apeglm"
$package
[1] "apeglm"
$version
[1] ‘1.16.0’
$prior.control
$prior.control$no.shrink
[1] 1
$prior.control$prior.mean
[1] 0
$prior.control$prior.scale
[1] 0.001
$prior.control$prior.df
[1] 1
$prior.control$prior.no.shrink.mean
[1] 0
$prior.control$prior.no.shrink.scale
[1] 15
$prior.control$prior.var
[1] 1e-06
priorInfo(resNorm)
$type
[1] "normal"
$package
[1] "DESeq2"
$version
[1] ‘1.34.0’
$betaPriorVar
Intercept conditiontreated
1.000000e+06 1.974018e-01
priorInfo(resAsh)
$type
[1] "ashr"
$package
[1] "ashr"
$version
[1] ‘2.2.51’
$fitted_g
$pi
[1] 0.9894591706 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
[9] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0057666315
[17] 0.0045680277 0.0000000000 0.0002061701 0.0000000000 0.0000000000 0.0000000000 0.0000000000
$mean
[1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
$sd
[1] 0.005907522 0.008354497 0.011815044 0.016708995 0.023630087 0.033417990 0.047260175 0.066835980
[9] 0.094520349 0.133671960 0.189040698 0.267343919 0.378081397 0.534687839 0.756162793 1.069375678
[17] 1.512325587 2.138751356 3.024651174 4.277502711 6.049302348 8.555005423 12.098604695
attr(,"class")
[1] "normalmix"
attr(,"row.names")
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
dispersionFunction(dds)
function (q)
coefs[1] + coefs[2]/q
<bytecode: 0x7fa76e1f23b8>
<environment: 0x7fa754a4a078>
attr(,"coefficients")
asymptDisp extraPois
0.8494044 4.5394083
attr(,"fitType")
[1] "parametric"
attr(,"varLogDispEsts")
[1] 1.20359
attr(,"dispPriorVar")
[1] 1.177617
attr(dispersionFunction(dds), "dispPriorVar")
[1] 1.177617
metadata(dds)[["version"]]
[1] ‘1.34.0’
normFactors <- matrix(runif(nrow(dds)*ncol(dds),0.5,1.5),
ncol=ncol(dds),nrow=nrow(dds),
dimnames=list(1:nrow(dds),1:ncol(dds)))
normFactors <- normFactors / exp(rowMeans(log(normFactors)))
normalizationFactors(dds) <- normFactors
coldata <- DataFrame(grp=factor(rep(c("X","Y"),each=6)),
ind=factor(rep(1:6,each=2)),
cnd=factor(rep(c("A","B"),6)))
coldata
DataFrame with 12 rows and 3 columns
grp ind cnd
<factor> <factor> <factor>
1 X 1 A
2 X 1 B
3 X 2 A
4 X 2 B
5 X 3 A
... ... ... ...
8 Y 4 B
9 Y 5 A
10 Y 5 B
11 Y 6 A
12 Y 6 B
as.data.frame(coldata)
coldata$ind.n <- factor(rep(rep(1:3,each=2),2))
as.data.frame(coldata)
model.matrix(~ grp + grp:ind.n + grp:cnd, coldata)
(Intercept) grpY grpX:ind.n2 grpY:ind.n2 grpX:ind.n3 grpY:ind.n3 grpX:cndB grpY:cndB
1 1 0 0 0 0 0 0 0
2 1 0 0 0 0 0 1 0
3 1 0 1 0 0 0 0 0
4 1 0 1 0 0 0 1 0
5 1 0 0 0 1 0 0 0
6 1 0 0 0 1 0 1 0
7 1 1 0 0 0 0 0 0
8 1 1 0 0 0 0 0 1
9 1 1 0 1 0 0 0 0
10 1 1 0 1 0 0 0 1
11 1 1 0 0 0 1 0 0
12 1 1 0 0 0 1 0 1
attr(,"assign")
[1] 0 1 2 2 2 2 3 3
attr(,"contrasts")
attr(,"contrasts")$grp
[1] "contr.treatment"
attr(,"contrasts")$ind.n
[1] "contr.treatment"
attr(,"contrasts")$cnd
[1] "contr.treatment"
W <- res$stat
maxCooks <- apply(assays(dds)[["cooks"]],1,max)
idx <- !is.na(W)
plot(rank(W[idx]), maxCooks[idx], xlab="rank of Wald statistic",
ylab="maximum Cook's distance per gene",
ylim=c(0,5), cex=.4, col=rgb(0,0,0,.3))
m <- ncol(dds)
p <- 3
abline(h=qf(.99, p, m - p))
plot(res$baseMean+1, -log10(res$pvalue),
log="x", xlab="mean of normalized counts",
ylab=expression(-log[10](pvalue)),
ylim=c(0,30),
cex=.4, col=rgb(0,0,0,.3))
use <- res$baseMean > metadata(res)$filterThreshold
h1 <- hist(res$pvalue[!use], breaks=0:50/50, plot=FALSE)
h2 <- hist(res$pvalue[use], breaks=0:50/50, plot=FALSE)
colori <- c(`do not pass`="khaki", `pass`="powderblue")
barplot(height = rbind(h1$counts, h2$counts), beside = FALSE,
col = colori, space = 0, main = "", ylab="frequency")
text(x = c(0, length(h1$counts)), y = 0, label = paste(c(0,1)),
adj = c(0.5,1.7), xpd=NA)
legend("topright", fill=rev(colori), legend=rev(names(colori)))
My next steps are clean-up and understanding the analysis. I also have to zip/tar my data file.
I will have to tar/zip my data file and share them on the Google Drive closer to the due date.